Bayesian Program
type: Class
subclass of: Character Based Program

Biogeographic Analysis Program
type: Class
subclass of: TreeAnalysisProgram

Bootstrapping Program
type: Class
subclass of: HypothesisValidationProgram

Branch And Bound Tree Search Program
type: Class
subclass of: HypothesisValidationProgram

Character based method
type: Class
subclass of: Phylogenetic inference method

Character Based Program
type: Class
subclass of: Phylogenetic Inference Program

Clocks Dating Stratigraphy Program
type: Class
subclass of: TreeAnalysisProgram

Comparative Method Analysis Program
type: Class
subclass of: TreeAnalysisProgram

Consensus Trees Program
type: Class
subclass of: HypothesisValidationProgram

DNA Model
type: Class
subclass of: Models

DNA Sequence
type: Class
subclass of: Nucleic Acid Sequence

Data Base
type: Class
subclass of: Source

Data Collection Program
type: Class
subclass of: 1. Data collection step

1. Data collection step
type: Class

Data Type
type: Class
subclass of: 1. Data collection step

Distance Based Method
type: Class
subclass of: Phylogenetic inference method

Distance Based Program
type: Class
subclass of: Phylogenetic Inference Program

Distance Matrix
type: Class
subclass of: Data Type

GTR
type: Class
subclass of: DNA Model
label: General Time Reversible

Gene Duplication And Genomic Analysis
type: Class
subclass of: ModelSelectionProgram

General MSA Program
type: Class
subclass of: Multiple Sequence Alignment Program

General purpose packages program
type: Class
subclass of: Data Collection Program
subclass of: HypothesisValidationProgram
subclass of: ModelSelectionProgram
subclass of: Phylogenetic Inference Program
subclass of: Multiple Sequence Alignment Program
subclass of: TreeAnalysisProgram
subclass of: TreeVisualizationProgram

Genome Sequence
type: Class
subclass of: Sequence Type

Global MSA Program
type: Class
subclass of: Multiple Sequence Alignment Program

Global PWA Program
type: Class
subclass of: Pairwise Alignment Program

HKY
type: Class
subclass of: DNA Model

Heuristic Search For Best Tree Program
type: Class
subclass of: Phylogenetic Inference Program

5. Hypothesis validation step
type: Class

Information Theory Based Program
type: Class
subclass of: Character Based Program

JC
type: Class
subclass of: DNA Model

JTT
type: Class
subclass of: Protein Model

Jones
type: Class
subclass of: Protein Model

K80
type: Class
subclass of: DNA Model

Local MSA Program
type: Class
subclass of: Multiple Sequence Alignment Program

Local PWA Program
type: Class
subclass of: Pairwise Alignment Program

Looking For Hybridization Or Recombination Events Program
type: Class
subclass of: TreeAnalysisProgram

Making Distances Program
type: Class
subclass of: Phylogenetic Inference Program

Maximum Likelihood Program
type: Class
subclass of: Character Based Program

Maximum Parsimony Program
type: Class
subclass of: Character Based Program

Phylogenetic inference method
type: Class
subclass of: 4. Phylogenetic inference step

Minimum Evolution Distance-Based Program
type: Class
subclass of: Distance Based Program

3. Model selection step
type: Class

MtArt
type: Class
subclass of: Protein Model

Multiple Sequence Alignment Program
type: Class
subclass of: Multiple Sequence Alignment Program

Neighbor-Joining Distance-Based Program
type: Class
subclass of: Distance Based Program

Nucleic Acid Sequence
type: Class
subclass of: Sequence Type

Other Disances-based Program
type: Class
subclass of: Distance Based Program

PAM
type: Class
subclass of: Protein Model

Pairwise Alignment Program
type: Class
subclass of: Data Collection Program

Phylogenetic Inference Program
type: Class
subclass of: 4. Phylogenetic inference step

4. Phylogenetic inference step
type: Class

Poisson Model
type: Class
subclass of: Protein Model

Protein Model
type: Class
subclass of: Models

Protein Sequence
type: Class
subclass of: Sequence Type

Quartets Program
type: Class
subclass of: Phylogenetic Inference Program

RNA Sequence
type: Class
subclass of: Nucleic Acid Sequence

SYM
type: Class
subclass of: DNA Model

Sequence
type: Class
subclass of: Sequence Type

Sequence Alignment
type: Class
subclass of: Sequence Type

Multiple Sequence Alignment Program
type: Class
subclass of: 2. Multiple sequence alignment step

2. Multiple sequence alignment step
type: Class

Sequence Management Program
type: Class
subclass of: Data Collection Program

Sequence Type
type: Class
subclass of: Data Type

Source
type: Class
subclass of: 1. Data collection step

T92
type: Class
subclass of: DNA Model

TN93
type: Class
subclass of: DNA Model

Tree
type: Class
subclass of: Data Type

6. Tree anlysis step
type: Class

Tree Plotting Darwing Program
type: Class
subclass of: TreeVisualizationProgram

Tree Simulation Program
type: Class
subclass of: Data Collection Program

7. Tree visualization step
type: Class

Number of bootstraps
type: Class
subclass of: ParametersBootstrappingProgram

F81 + G
type: NamedIndividual
type: F81
label: F81 + I
label: F81 + I + G
label: F81 + gamma
label: F81+G
label: F81+I+G
label: F81+gamma

JC + P + I
type: NamedIndividual
type: JC
label: JC + gamma
label: JC+G
label: JC+I
label: JC+P
label: JC+P+I
label: JC+gamma

JC
type: NamedIndividual
label: Jukes and Cantor

K80
type: NamedIndividual
label: Kimura

K80 + G
type: NamedIndividual
type: K80
label: K80 + I + G
label: K80+G
label: K80+I+G

SYM + G
type: NamedIndividual
type: SYM
label: SYM + I
label: SYM + I + G
label: SYM + I + P
label: SYM + gamma
label: SYM+G
label: SYM+I
label: SYM+I+G
label: SYM+I+P
label: SYM+gamma

SYM
type: NamedIndividual
label: Symmetrical model

JTT
type: NamedIndividual

PAM
type: NamedIndividual

WAG
type: NamedIndividual
label: WAG + G
label: WAG + I
label: WAG + I + G
label: WAG+G
label: WAG+I
label: WAG+I+G

Poisson
type: NamedIndividual
type: Poisson Model
label: Poisson model

Jones
type: NamedIndividual

LG
type: NamedIndividual
label: LG + G
label: LG + I
label: LG + I + G
label: LG+G
label: LG+I
label: LG+I+G

MtArt
type: NamedIndividual

T92
type: NamedIndividual

TN93
type: NamedIndividual

GTR + G
type: NamedIndividual
type: GTR
label: GTR + I
label: GTR + I + G
label: GTR + gamma
label: GTR+G
label: GTR+I
label: GTR+I+G
label: GTR+gamma

GTR
type: NamedIndividual
label: Generalised time-reversible
label: general time reversible

HKY
type: NamedIndividual
label: Hasegawa, Kishino and Yano

HKI + I
type: NamedIndividual
type: HKY
label: HKI + P
label: HKI + P + I
label: HKI + g
label: HKI + gamma
label: HKI+I
label: HKI+P
label: HKI+g
label: HKI+gamma
label: HKY+P+I

ABA
type: NamedIndividual
type: Global MSA Program
description: A-Bruijn alignment

Compass
type: NamedIndividual
type: Global MSA Program
description: COmparison of Multiple Protein sequence Alignments with assessment of Statistical Significance

PSI-BLAST
type: NamedIndividual
type: Global PWA Program

BLASTX
type: NamedIndividual
type: Global PWA Program

TBLASTX
type: NamedIndividual
type: Global PWA Program

megaBLAST
type: NamedIndividual
type: Global PWA Program

PSI-BLAST
type: NamedIndividual
type: Global PWA Program

RPSBLAST
type: NamedIndividual
type: Global PWA Program

DELTA-BLAST
type: NamedIndividual
type: Global PWA Program

TBLASTN
type: NamedIndividual
type: Global PWA Program

DECIPHER
type: NamedIndividual
type: Global MSA Program
description: Progressive/iterative alignment

DIALIGN-TX
type: NamedIndividual
type: General MSA Program
description: Segment-based method

DNA Alignment
type: NamedIndividual
type: General MSA Program
description: Segment-based method for intraspecific alignments

DNA Baser Sequence Assembler
type: NamedIndividual
type: General MSA Program
description: Multi alignment; Automatic batch alignment

EDNA
type: NamedIndividual
type: General MSA Program
description: Energy Based Multiple Sequence Alignment for DNA Binding Sites

FSA
type: NamedIndividual
type: Global MSA Program
description: Sequence annealing

Geneious
type: NamedIndividual
type: General MSA Program
description: Progressive/Iterative alignment; ClustalW plugin

Kalign
type: NamedIndividual
type: Global MSA Program
description: Progressive alignment

MAFFT
type: NamedIndividual
type: General MSA Program
description: Progressive/iterative alignment

ALE
type: NamedIndividual
type: Local MSA Program
description: manual alignment ; some software assistance

MARNA
type: NamedIndividual
type: Local MSA Program
description: Multiple Alignment of RNAs

MAVID
type: NamedIndividual
type: Global MSA Program
description: Progressive alignment

MSA
type: NamedIndividual
type: General MSA Program
description: Dynamic programming

MSAProbs
type: NamedIndividual
type: Global MSA Program
description: Dynamic programming

MULTALIN
type: NamedIndividual
type: General MSA Program
description: Dynamic programming/clustering

Multi-LAGAN
type: NamedIndividual
type: Global MSA Program
description: Progressive dynamic programming alignment

MUSCLE
type: NamedIndividual
type: General MSA Program
description: Progressive/iterative alignment

Opal
type: NamedIndividual
type: General MSA Program
description: Progressive/iterative alignment

Pecan
type: NamedIndividual
type: Global MSA Program
description: Probabilistic/consistency

Phylo
type: NamedIndividual
type: General MSA Program
description: A human computing framework for comparative genomics to solve multiple alignment

AMAP
type: NamedIndividual
type: Global MSA Program
description: Sequence annealing

Praline
type: NamedIndividual
type: Global MSA Program
description: Progressive/iterative/consistency/homology-extended alignment with pre-profiling and secondary structure prediction

PicXAA
type: NamedIndividual
type: Global MSA Program
description: non-progressive/maximum expected accuracy alignment

POA
type: NamedIndividual
type: General MSA Program
description: Partial order/hidden Markov model

Probalign
type: NamedIndividual
type: Global MSA Program
description: Probabilistic/consistency with partition function probabilities

ProbCons
type: NamedIndividual
type: General MSA Program
description: Probabilistic/consistency

PROMALS3D
type: NamedIndividual
type: Global MSA Program
description: Progressive alignment/hidden Markov model/Secondary structure/3D structure

PRRN
type: NamedIndividual
type: General MSA Program
description: Iterative alignment (especially refinement)

PSAlign
type: NamedIndividual
type: General MSA Program
description: Alignment preserving non-heuristic

RevTrans
type: NamedIndividual
type: General MSA Program
description: Combines DNA and Protein alignment by back translating the protein alignment to DNA.

SAGA
type: NamedIndividual
type: General MSA Program
description: Sequence alignment by genetic algorithm

anon.
type: NamedIndividual
type: Global MSA Program
description: fast optimal alignment of three sequences using linear gap costs

SAM
type: NamedIndividual
type: General MSA Program
description: Hidden Markov model

Se-Al
type: NamedIndividual
type: Local MSA Program
description: Manual alignment

StatAlign
type: NamedIndividual
type: Global MSA Program
description: Bayesian co-estimation of alignment and phylogeny (MCMC)

Stemloc
type: NamedIndividual
type: General MSA Program
description: Multiple alignment and secondary structure prediction

T-Coffee
type: NamedIndividual
type: General MSA Program
description: More sensitive progressive alignment

UGENE
type: NamedIndividual
type: General MSA Program
description: Supports multiple alignment with MUSCLE KAlign Clustal and MAFFT plugins

VectorFriends
type: NamedIndividual
type: General MSA Program
description: VectorFriends Aligner MUSCLE plugin and ClustalW plugin

GLProbs
type: NamedIndividual
type: Global MSA Program
description: Adaptive pair-Hidden Markov Model based approach

DIALIGN-T
type: NamedIndividual
type: General MSA Program
description: Segment-based method

PRRP
type: NamedIndividual
type: General MSA Program
description: Iterative alignment (especially refinement)

BAli-Phy
type: NamedIndividual
type: Global MSA Program
description: Tree+Multi alignment ; Probabilistic/Bayesian ; Joint Estimation

ACANA
type: NamedIndividual
type: Global PWA Program
description: fast heuristic anchor based pairwise alignment

AlignMe
type: NamedIndividual
type: Global PWA Program
description: Alignments for membrane protein sequences

Bioconductor
type: NamedIndividual
type: Global PWA Program
description: Dynamic programming

BioPerl dpAlign
type: NamedIndividual
type: Global PWA Program
description: Dynamic programming

BLASTZ
type: NamedIndividual
type: Local PWA Program
description: Seeded pattern-matching

CUDAlign
type: NamedIndividual
type: Global PWA Program
description: DNA sequence alignment of unrestricted size in single or multiple GPUs

FEAST
type: NamedIndividual
type: Local PWA Program
description: Posterior based local extension with descriptive evolution model

Base-By-Base
type: NamedIndividual
type: General MSA Program
description: Java-based multiple sequence alignment editor with integrated analysis tools

G-PAS
type: NamedIndividual
type: Global PWA Program
description: GPU-based dynamic programming with backtracking

JAligner
type: NamedIndividual
type: Local PWA Program
description: Open source Java implementation of Smith-Waterman

K*Sync
type: NamedIndividual
type: Global PWA Program
description: Protein sequence to structure alignment that includes secondary structure structural conservation structure-derived sequence profiles and consensus alignment scores

mAlign
type: NamedIndividual
type: Global PWA Program
description: modelling alignment; models the information content of the sequences

matcher
type: NamedIndividual
type: Local PWA Program
description: Waterman-Eggert local alignment (based on LALIGN)

Path
type: NamedIndividual
type: Local PWA Program
description: Smith-Waterman on protein back-translation graph (detects frameshifts at protein level)

PatternHunter
type: NamedIndividual
type: Local PWA Program
description: Seeded pattern-matching

REPuter
type: NamedIndividual
type: Local PWA Program
description: suffix tree based

Satsuma
type: NamedIndividual
type: Local PWA Program
description: Parallel whole-genome synteny alignments

ClustalW
type: NamedIndividual
type: General MSA Program
description: Progressive alignment
label: Clustal Omega
label: Clustal W
label: Clustal X
label: ClustalX

SEQALN
type: NamedIndividual
type: Global PWA Program
description: Various dynamic programming

SIM
type: NamedIndividual
type: Global PWA Program
description: Local similarity with varying gap treatments

GAP
type: NamedIndividual
type: Local PWA Program
description: Local similarity

SSEARCH
type: NamedIndividual
type: Local PWA Program
description: Local (Smith-Waterman) alignment with statistics

Sequences Studio
type: NamedIndividual
type: Global PWA Program
description: Java applet demonstrating various algorithms from [18]

SWIFT suit
type: NamedIndividual
type: Local PWA Program
description: Fast Local Alignment Searching

tranalign
type: NamedIndividual
type: Global PWA Program
description: Aligns nucleic acid sequences given a protein alignment

UGENE
type: NamedIndividual
type: Global PWA Program
description: Opensource Smith-Waterman for SSE/CUDA Suffix array based repeats finder & dotplot

CodonCode Aligner
type: NamedIndividual
type: General MSA Program
description: Multi alignment; ClustalW & Phrap support

water
type: NamedIndividual
type: Local PWA Program
description: Smith-Waterman dynamic programming

wordmatch
type: NamedIndividual
type: Global PWA Program
description: k-tuple pairwise match

YASS
type: NamedIndividual
type: Local PWA Program
description: Seeded pattern-matching

LASTZ
type: NamedIndividual
type: Local PWA Program
description: Seeded pattern-matching

NAP
type: NamedIndividual
type: Global PWA Program
description: Local similarity with varying gap treatments

BLAST
type: NamedIndividual
type: Global PWA Program

BLASTP
type: NamedIndividual
type: Global PWA Program

BLASTN
type: NamedIndividual
type: Global PWA Program

WU-BLAST
type: NamedIndividual
type: Global PWA Program

tree
type: NamedIndividual
type: Tree
has aligned by: DIALIGN-TX
has aligned by: Geneious
has aligned by: MAFFT
has aligned by: MSA
has aligned by: MULTALIN
has aligned by: MUSCLE
has aligned by: Phylo
has aligned by: SAGA
has aligned by: UGENE
has aligned by: ClustalW
has aligned by: MEGA
has aligned by: MrBayes
has aligned by: PAUP
has aligned by: PHYLIP
has aligned by: PHYML
has aligned by: RAxML
has aligned by: ClustalW2
has aligned by: Clustal
has aligned by: ClustalV
has collected by: BLASTX
has collected by: DELTA-BLAST
has collected by: UGENE
has collected by: water
has collected by: BLAST
has collected by: BLASTP
has collected by: BLASTN
has collected by: WU-BLAST
has collected by: BioEdit
has collected by: MEGA
has collected by: MrBayes
has collected by: PHYML
has collected by: DNADIST
has collected by: PROTDIST
has collected by: SEQBOOT
has hypothesis validated by: APE
has hypothesis validated by: ARB
has hypothesis validated by: BEAST
has hypothesis validated by: Bio++
has hypothesis validated by: Clann
has hypothesis validated by: CONSEL
has hypothesis validated by: DendroPy
has hypothesis validated by: ELW
has hypothesis validated by: FastME
has hypothesis validated by: Geneious
has hypothesis validated by: MacClade
has hypothesis validated by: MEGA
has hypothesis validated by: MESA
has hypothesis validated by: Mesquite
has hypothesis validated by: ModelTest
has hypothesis validated by: Modeltest
has hypothesis validated by: MrBayes
has hypothesis validated by: MrModeltest
has hypothesis validated by: Notung
has hypothesis validated by: PAML
has hypothesis validated by: PAUP
has hypothesis validated by: PHASE
has hypothesis validated by: PHYLIP
has hypothesis validated by: PhyloBayes
has hypothesis validated by: PHYML
has hypothesis validated by: PhySIC_IST
has hypothesis validated by: Phyutility
has hypothesis validated by: ProtTest
has hypothesis validated by: RAxML
has hypothesis validated by: raxmlGUI
has hypothesis validated by: SeaView
has hypothesis validated by: SuperTree
has hypothesis validated by: tracer
has hypothesis validated by: TREECON
has hypothesis validated by: Treefinder
has hypothesis validated by: TREEMAP
has hypothesis validated by: UGENE
has hypothesis validated by: CONTRAST
has hypothesis validated by: PENNY
has hypothesis validated by: Nearest Neighbor Interchange
has hypothesis validated by: SPR
has inferred by: analysis
has inferred by: ANC-GENE
has inferred by: Ancestor

alignment
type: NamedIndividual
type: Sequence Alignment
has aligned by: Geneious
has aligned by: Kalign
has aligned by: MAFFT
has aligned by: MSA
has aligned by: MULTALIN
has aligned by: MUSCLE
has aligned by: Opal
has aligned by: Phylo
has aligned by: PROMALS3D
has aligned by: RevTrans
has aligned by: SAM
has aligned by: Se-Al
has aligned by: T-Coffee
has aligned by: BAli-Phy
has aligned by: ClustalW
has aligned by: ALIGN
has aligned by: DAMBE
has aligned by: GeneDoc
has aligned by: MacClade
has aligned by: PAUP
has aligned by: PHYLIP
has aligned by: SeaView
has aligned by: ClustalW2
has aligned by: Clustal
has aligned by: ClustalV
has collected by: BLASTX
has collected by: BLAST
has collected by: BLASTP
has collected by: BLASTN
has collected by: BioEdit
has collected by: MEGA
has collected by: PHYDIT
has collected by: PHYLIP
has collected by: PROTDIST
has collected by: SEQBOOT
has hypothesis validated by: ARB
has hypothesis validated by: DAMBE
has hypothesis validated by: ELW
has hypothesis validated by: Geneious
has hypothesis validated by: MEGA
has hypothesis validated by: ModelTest
has hypothesis validated by: PAUP
has hypothesis validated by: PHYLIP
has hypothesis validated by: PHYML
has hypothesis validated by: RAxML
has hypothesis validated by: SeaView
has hypothesis validated by: TCS
has hypothesis validated by: Treefinder
has inferred by: analysis
has inferred by: ARB
has inferred by: BAli-Phy
has inferred by: BEAST
has inferred by: BEST
has inferred by: Bio++
has inferred by: BIONJ
has inferred by: Bionumerics
has inferred by: Bosque
has inferred by: DAMBE
has inferred by: DISTANCE
has inferred by: DnaSP
has inferred by: EMBOSS
has inferred by: FastTree
has inferred by: GARLI
has inferred by: Geneious
has inferred by: MacClade
has inferred by: MacVector
has inferred by: MEGA
has inferred by: Mesquite
has inferred by: ModelGenerator
has inferred by: Modeltest
has inferred by: MOLPHY
has inferred by: MrBayes
has inferred by: MrModeltest
has inferred by: Network
has inferred by: PAML
has inferred by: PAUP
has inferred by: PHYLIP
has inferred by: PhyloBayes

Genomes
type: NamedIndividual
type: Genome Sequence
has aligned by: Geneious
has aligned by: MAFFT
has aligned by: MUSCLE
has aligned by: SAGA
has aligned by: ClustalW
has aligned by: MEGA
has collected by: BLASTX
has collected by: TBLASTX
has collected by: TBLASTN
has collected by: BLAST
has collected by: BLASTP
has collected by: BLASTN
has collected by: WU-BLAST
has collected by: BioEdit
has collected by: FACTOR
has hypothesis validated by: MEGA
has hypothesis validated by: ModelTest
has hypothesis validated by: PAML
has inferred by: analysis
has inferred by: BEAST
has inferred by: BIONJ
has inferred by: COMPARE
has inferred by: COMPONENT
has inferred by: DAMBE
has inferred by: FastTree
has inferred by: FootPrinter
has inferred by: Geneious
has inferred by: MacVector
has inferred by: MEGA
has inferred by: Modeltest
has inferred by: MrBayes
has inferred by: PAML
has inferred by: PAUP
has inferred by: PHYLIP
has inferred by: PHYML
has inferred by: Phyutility
has inferred by: RA
has inferred by: RAxML
has inferred by: Simplot
has inferred by: SplitsTree
has inferred by: TNT
has inferred by: tracer
has inferred by: DNAPARS
has inferred by: PARS
has retrieved in data base: NCBI
has retrieved in data base: RefSeq
has retrieved in data base: SOURCE
has retrieved in data base: EMBL
has retrieved in data base: ENCODE
has retrieved in data base: Ensembl
has retrieved in data base: GenBank
has retrieved in data base: Flybase
has retrieved in data base: SEED
has retrieved in data base: Wormbase
has retrieved in data base: TAIR
has retrieved in data base: Pfam
has retrieved in data base: SUPERFAMILY
has retrieved in data base: Entrez
has tree analyzed by: PHYLIP
has tree analyzed by: Simplot
has tree visualized by: FigTree
label: genome
label: genome sequence
label: genome sequences
label: metagenomic
label: metagenomic sequence
label: metagenomic sequences

rrs sequence
type: NamedIndividual
type: Sequence
has aligned by: MUSCLE

RNA
type: NamedIndividual
type: RNA Sequence
has aligned by: MAFFT
has aligned by: MULTALIN
has aligned by: MUSCLE
has aligned by: ClustalW
has aligned by: ARB
has aligned by: MEGA
has aligned by: SeqPup
has aligned by: ClustalW2
has collected by: PSI-BLAST
has collected by: TBLASTN
has collected by: BLAST
has collected by: BLASTP
has collected by: PROTDIST
has inferred by: ARB
has inferred by: BayesPhylogenies
has inferred by: FastTree
has inferred by: MEGA
has inferred by: MrBayes
has inferred by: MrModeltest
has inferred by: PHASE
has inferred by: PHYLIP
has inferred by: RAxML
has inferred by: SeaView
has inferred by: SeqPup
has inferred by: TOPALi
has retrieved in data base: BIND
has retrieved in data base: NCBI
has retrieved in data base: RefSeq
has retrieved in data base: GenBank
has retrieved in data base: RDP
has tree analyzed by: RDP3
label: RNA sequences
label: ribosomal
label: ribosomal sequence
label: ribosomal sequences

DNA
type: NamedIndividual
type: DNA Sequence
label: DNA sequence
label: DNA sequences
label: Deoxyribonucleic acid
label: Deoxyribonucleic acid sequence
label: Deoxyribonucleic acid sequences

nuclear SSU
type: NamedIndividual
type: Sequence
has inferred by: PAUP

Nucleotide
type: NamedIndividual
type: Nucleic Acid Sequence
has aligned by: Geneious
has aligned by: MAFFT
has aligned by: MULTALIN
has aligned by: MUSCLE
has aligned by: RevTrans
has aligned by: Se-Al
has aligned by: T-Coffee
has aligned by: DIALIGN-T
has aligned by: ClustalW
has aligned by: ALIGN
has aligned by: Bio++
has aligned by: DAMBE
has aligned by: MacClade
has aligned by: MEGA
has aligned by: ClustalW2
has aligned by: Clustal
has collected by: BLASTX
has collected by: megaBLAST
has collected by: BLAST
has collected by: BLASTP
has collected by: BLASTN
has collected by: BioEdit
has collected by: MEGA
has collected by: MrBayes
has collected by: DNADIST
has collected by: PROTDIST
has collected by: SEQBOOT
has hypothesis validated by: DAMBE
has hypothesis validated by: Geneious
has hypothesis validated by: MEGA
has hypothesis validated by: ModelGenerator
has hypothesis validated by: ModelTest
has hypothesis validated by: Modeltest
has hypothesis validated by: PAUP
has hypothesis validated by: PHYLIP
has hypothesis validated by: PHYML
has hypothesis validated by: RAxML
has hypothesis validated by: raxmlGUI
has hypothesis validated by: TreeRot
has hypothesis validated by: PENNY
has inferred by: analysis
has inferred by: ARB
has inferred by: BEAST
has inferred by: BEST
has inferred by: Bio++
has inferred by: BIONJ
has inferred by: Bionumerics
has inferred by: CONSEL
has inferred by: DAMBE
has inferred by: Darwin
has inferred by: DISTANCE
has inferred by: DNASIS
has inferred by: DnaSP
has inferred by: EMBOSS
has inferred by: FastTree
has inferred by: GARLI
has inferred by: Geneious
has inferred by: Kakusan4
has inferred by: MacClade
has inferred by: MacVector
has inferred by: MEGA
has inferred by: ModelGenerator
has inferred by: Modeltest
has inferred by: MrBayes
has inferred by: MrModeltest
has inferred by: PAML
has inferred by: PAUP
has inferred by: PHYLIP
has inferred by: PhyloBayes
has inferred by: PHYML
has inferred by: ProtTest
has inferred by: RAxML
has inferred by: raxmlGUI
has inferred by: SeaView
has inferred by: SLR
has inferred by: TipDate
has inferred by: TOPALi

Amino acid
type: NamedIndividual
type: Protein Sequence
has aligned by: Geneious
has aligned by: Kalign
has aligned by: MAFFT
has aligned by: MSA
has aligned by: MULTALIN
has aligned by: MUSCLE
has aligned by: Praline
has aligned by: Probalign
has aligned by: ProbCons
has aligned by: PROMALS3D
has aligned by: RevTrans
has aligned by: Se-Al
has aligned by: T-Coffee
has aligned by: DIALIGN-T
has aligned by: ClustalW
has aligned by: DAMBE
has aligned by: EMBOSS
has aligned by: GeneDoc
has aligned by: MacClade
has aligned by: MEGA
has aligned by: Mesquite
has aligned by: MrBayes
has aligned by: PAUP
has aligned by: PHYLIP
has aligned by: PHYML
has aligned by: RAxML
has aligned by: SeaView
has aligned by: ClustalW2
has aligned by: Clustal
has aligned by: ClustalV
has aligned by: EMMA
has collected by: PSI-BLAST
has collected by: BLASTX
has collected by: TBLASTX
has collected by: DELTA-BLAST
has collected by: TBLASTN
has collected by: water
has collected by: BLAST
has collected by: BLASTP
has collected by: WU-BLAST
has collected by: BioEdit
has collected by: DNADIST
has collected by: PROTDIST
has collected by: SEQBOOT
has hypothesis validated by: CONSEL
has hypothesis validated by: Geneious
has hypothesis validated by: MEGA
has hypothesis validated by: ModelTest
has hypothesis validated by: MrBayes
has hypothesis validated by: PAUP
has hypothesis validated by: PHYLIP
has hypothesis validated by: PhyloBayes
has hypothesis validated by: PHYML
has hypothesis validated by: ProtTest
has hypothesis validated by: RAxML
has hypothesis validated by: Nearest Neighbor Interchange
has hypothesis validated by: SPR
has inferred by: analysis
has inferred by: ARB
has inferred by: BEAST
has inferred by: BEST
has inferred by: BIONJ
has inferred by: Bionumerics
has inferred by: Bosque
has inferred by: CONSEL
has inferred by: DAMBE
has inferred by: Darwin
has inferred by: DISTANCE
has inferred by: DNASIS
has inferred by: EMBOSS
has inferred by: FastTree
has inferred by: GARLI
has inferred by: Geneious
has inferred by: MacClade
has inferred by: MacVector
has inferred by: MEGA

restriction site
type: NamedIndividual
type: Sequence
has inferred by: MrBayes
label: restriction sites

distance matrices
type: NamedIndividual
type: Distance Matrix
has aligned by: ClustalW
has collected by: DNADIST
has collected by: PROTDIST
has hypothesis validated by: FastME
has hypothesis validated by: MEGA
has hypothesis validated by: TREECON
has inferred by: analysis
has inferred by: BIONJ
has inferred by: DISTANCE
has inferred by: FastME
has inferred by: MacVector
has inferred by: MEGA
has inferred by: ModelGenerator
has inferred by: PAUP
has inferred by: PHYLIP
has inferred by: QuickTree
has inferred by: SplitsTree
has inferred by: START2
has inferred by: TREE-PUZZLE
has inferred by: TREECON
has inferred by: FITCH
has inferred by: NEIGHBOR
has retrieved in data base: GenBank
has retrieved in data base: SEED
has tree analyzed by: START2
has tree visualized by: PhyloWidget
has tree visualized by: CONSENSE
label: distance matrix

DNA Data Bank of Japan
type: NamedIndividual
type: InternationalNucleotideSequenceDatabase

euGenes
type: NamedIndividual
type: Metadatabases

SRPDB
type: NamedIndividual
type: RNADatabases

yeast snoRNA
type: NamedIndividual
type: RNADatabases

Sno/scaRNAbase
type: NamedIndividual
type: RNADatabases

snoRNA-LBME-db
type: NamedIndividual
type: RNADatabases

EuroCarbDB
type: NamedIndividual
type: CarbohydrateStructureDatabases

BIND
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

BioGRID
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

CCSB Interactome
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

DIP
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

IntAct molecular interaction database
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

GeneCards
type: NamedIndividual
type: Metadatabases

NetPro
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

STRING
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

The Cell Collective
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

MINT
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

iRefIndex
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

RNA-binding
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

BioLiP
type: NamedIndividual
type: ProteinProteinAndOtherMolecularInteractions

MetaboLights
type: NamedIndividual
type: MetabolomicDatabases

HMDB
type: NamedIndividual
type: MetabolomicDatabases

YMDB
type: NamedIndividual
type: MetabolomicDatabases

MetaBase
type: NamedIndividual
type: Metadatabases

ECMDB
type: NamedIndividual
type: MetabolomicDatabases

DrugBank
type: NamedIndividual
type: MetabolomicDatabases

ChEBI
type: NamedIndividual
type: MetabolomicDatabases

BioMagResBank
type: NamedIndividual
type: MetabolomicDatabases

Golm Metabolome Database
type: NamedIndividual
type: MetabolomicDatabases

MassBank
type: NamedIndividual
type: MetabolomicDatabases

NCBI
type: NamedIndividual

RefSeq
type: NamedIndividual
type: NCBI

Unigene
type: NamedIndividual
type: NCBI

Uniprot
type: NamedIndividual
type: NCBI

mGen
type: NamedIndividual
type: Metadatabases

MOPED
type: NamedIndividual
type: Metadatabases

PathogenPortal
type: NamedIndividual
type: Metadatabases

SOURCE
type: NamedIndividual
type: Metadatabases

iRefIndex
type: NamedIndividual
type: Metadatabases

Pathway Commons
type: NamedIndividual
type: Metadatabases

Nowomics
type: NamedIndividual
type: Metadatabases

EMBL
type: NamedIndividual
type: InternationalNucleotideSequenceDatabase

BioGPS
type: NamedIndividual
type: Metadatabases

ENCODE
type: NamedIndividual
type: Metadatabases

Human Epigenome Atlas
type: NamedIndividual
type: Metadatabases

Bioinformatic Harvester
type: NamedIndividual
type: GenomeDatabases

Gene Disease Database
type: NamedIndividual
type: GenomeDatabases

SNPedia
type: NamedIndividual
type: GenomeDatabases

CAMERA
type: NamedIndividual
type: GenomeDatabases

Corn
type: NamedIndividual
type: GenomeDatabases

EcoCyc
type: NamedIndividual
type: GenomeDatabases

Ensembl
type: NamedIndividual
type: GenomeDatabases

GenBank
type: NamedIndividual
type: InternationalNucleotideSequenceDatabase

Ensembl Genomes
type: NamedIndividual
type: GenomeDatabases

PATRIC
type: NamedIndividual
type: GenomeDatabases

Flybase
type: NamedIndividual
type: GenomeDatabases

MGI Mouse Genome
type: NamedIndividual
type: GenomeDatabases

JGI Genomes
type: NamedIndividual
type: GenomeDatabases

National Microbial Pathogen Data Resource
type: NamedIndividual
type: GenomeDatabases

RegulonDB
type: NamedIndividual
type: GenomeDatabases

Repbase
type: NamedIndividual
type: GenomeDatabases

Saccharomyces Genome Database
type: NamedIndividual
type: GenomeDatabases

Viral Bioinformatics Resource Center
type: NamedIndividual
type: GenomeDatabases

BioGraph
type: NamedIndividual
type: Metadatabases

SEED
type: NamedIndividual
type: GenomeDatabases

Xenbase
type: NamedIndividual
type: GenomeDatabases

Wormbase
type: NamedIndividual
type: GenomeDatabases

Zebrafish Information Network
type: NamedIndividual
type: GenomeDatabases

TAIR
type: NamedIndividual
type: GenomeDatabases

UCSC Malaria Genome Browser
type: NamedIndividual
type: GenomeDatabases

RGD Rat Genome Database
type: NamedIndividual
type: GenomeDatabases

INTEGRALL
type: NamedIndividual
type: GenomeDatabases

Fourmidable ant genome database
type: NamedIndividual
type: GenomeDatabases

VectorBase
type: NamedIndividual
type: GenomeDatabases

Bioinformatic Harvester
type: NamedIndividual
type: Metadatabases

EzGenome
type: NamedIndividual
type: GenomeDatabases

Banana Genome Hub
type: NamedIndividual
type: GenomeDatabases

GeneDB
type: NamedIndividual
type: GenomeDatabases

EuPathDB
type: NamedIndividual
type: GenomeDatabases

SNiPhunter
type: NamedIndividual
type: GenomeDatabases

1000 Genomes
type: NamedIndividual
type: GenomeDatabases

Personal Genome Project
type: NamedIndividual
type: GenomeDatabases

UniProt
type: NamedIndividual
type: ProteinSequenceDatabases

Protein Information Resource
type: NamedIndividual
type: ProteinSequenceDatabases

Swiss-Prot Protein
type: NamedIndividual
type: ProteinSequenceDatabases

Neuroscience Information Framework
type: NamedIndividual
type: Metadatabases

PEDANT
type: NamedIndividual
type: ProteinSequenceDatabases

PROSITE
type: NamedIndividual
type: ProteinSequenceDatabases

Database of Interacting Proteins
type: NamedIndividual
type: ProteinSequenceDatabases

Pfam
type: NamedIndividual
type: ProteinSequenceDatabases

PRINT
type: NamedIndividual
type: ProteinSequenceDatabases

ProDom
type: NamedIndividual
type: ProteinSequenceDatabases

SignalP 3.0
type: NamedIndividual
type: ProteinSequenceDatabases

SUPERFAMILY
type: NamedIndividual
type: ProteinSequenceDatabases

Annotation Clearing House
type: NamedIndividual
type: ProteinSequenceDatabases

InterPro
type: NamedIndividual
type: ProteinSequenceDatabases

ConsensusPathDB
type: NamedIndividual
type: Metadatabases

ProteomeScout
type: NamedIndividual
type: ProteinSequenceDatabases

PRIDE
type: NamedIndividual
type: ProteomicsDatabases

ProteomeScout
type: NamedIndividual
type: ProteomicsDatabases

MitoMiner
type: NamedIndividual
type: ProteomicsDatabases

GelMap
type: NamedIndividual
type: ProteomicsDatabases

ProteomeXchange
type: NamedIndividual
type: ProteomicsDatabases

PDB
type: NamedIndividual

PDBe
type: NamedIndividual
type: PDB

PDBj
type: NamedIndividual
type: PDB

PDB
type: NamedIndividual

Entrez
type: NamedIndividual
type: Metadatabases

SCOP
type: NamedIndividual
type: ProteinStructureDatabases

CATH
type: NamedIndividual
type: ProteinStructureDatabases

PDBsum
type: NamedIndividual
type: ProteinStructureDatabases

Swiss-model
type: NamedIndividual
type: ProteinModelDatabases

ModBase
type: NamedIndividual
type: ProteinModelDatabases

PMP
type: NamedIndividual
type: ProteinModelDatabases

SIMAP
type: NamedIndividual
type: ProteinModelDatabases

C-It-Loci
type: NamedIndividual
type: RNADatabases

LncRNAWiki
type: NamedIndividual
type: RNADatabases

Rfam
type: NamedIndividual
type: RNADatabases

Enzyme Portal
type: NamedIndividual
type: Metadatabases

miRBase
type: NamedIndividual
type: RNADatabases

snoRNAdb
type: NamedIndividual
type: RNADatabases

lncRNAdb
type: NamedIndividual
type: RNADatabases

DASHR
type: NamedIndividual
type: RNADatabases

MONOCLdb
type: NamedIndividual
type: RNADatabases

piRNAbank
type: NamedIndividual
type: RNADatabases

GtRNAdb
type: NamedIndividual
type: RNADatabases

SILVA
type: NamedIndividual
type: RNADatabases

RDP
type: NamedIndividual
type: RNADatabases

tmRDB
type: NamedIndividual
type: RNADatabases

BI
type: NamedIndividual
type: Character based method
label: Bayesian
label: Bayesian analysis
label: Bayesian method
label: bayesian inference

ML
type: NamedIndividual
type: Character based method
label: Maximum Likelihood
label: Maximum-Likelihood
label: likelihood
label: maximum likelihood
label: maximum-likelihood

Likelihood
type: NamedIndividual
type: Character based method
label: MP
label: Maximum Parsimony
label: Parsimony
label: maximum parsimony
label: maximum-parsimony

Distance Wagner
type: NamedIndividual
type: Distance Based Method

NJ
type: NamedIndividual
type: Distance Based Method
label: Neighbour-joining
label: neighbor joining
label: neighbor-joining

UPGMA
type: NamedIndividual
type: Distance Based Method
label: Unweighted Pair-Group Method with Arithmethic Averaging

Bayesian Markov Chain Monte Carlo
type: NamedIndividual
type: Character based method
label: MCMC
label: Markov Chain Monte Carlo

ALIFRITZ
type: NamedIndividual
type: General purpose packages program
label: Statistical Multiple Alignment and Phylogeny Reconstruction

ALIGN
type: NamedIndividual
type: General MSA Program

AMBIORE
type: NamedIndividual
type: Bayesian Program
description: This software implements a flexible and computationally efficient Bayesian Markov chain Monte Carlo approach to estimating rates in evolution given a sequence alignment and tree topology relating the species. The evolutionary model allows substitution rates at a site to depend on the two flanking nucleotides, the branch of the phylogenetic tree, and position within a sequence. The package [220K] includes C source code and documentation. Reference: Hwang DG and Green P: Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proceedings of the National Academy of Sciences U.S.A. 101:13994-4001, Epub Aug. 03 (2004).
label: Applications for MCMC Bayesian Inference of Rates in Evolution

analysis
type: NamedIndividual
type: Making Distances Program
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ
has phylogenetic method: Bayesian Markov Chain Monte Carlo

ANC-GENE
type: NamedIndividual
type: Bayesian Program

Ancestor
type: NamedIndividual
type: Other Disances-based Program
has phylogenetic method: BI
has phylogenetic method: ML

ANCML
type: NamedIndividual
type: Comparative Method Analysis Program

APE
type: NamedIndividual
type: General purpose packages program

apTreeshape
type: NamedIndividual
type: General purpose packages program

ARB
type: NamedIndividual
type: General purpose packages program
has evolutionary model: K80
has evolutionary model: HKY
has phylogenetic method: ML
has phylogenetic method: Likelihood

ArboDraw
type: NamedIndividual
type: General purpose packages program

Archaeopteryx
type: NamedIndividual
type: Tree Plotting Darwing Program

Arlequin
type: NamedIndividual
type: Other Disances-based Program

AutoDecay
type: NamedIndividual
type: Bootstrapping Program
description: Torsten Eriksson of the Bergius Botanical Garden, Stockholm, Sweden (torsten (at) bergianska.se) has written a program, AutoDecay which generates Decay Indices from an existing PAUP 4.0 treefile. It is intended to simplify the the task of creating reverse constraint trees in PAUP 4.0 and subsequent generation of Bremer support values. (Bremer, K. 1994. Cladistics 10: 295-304). AutoDecay version 5.06 is written in the scripting language Perl, and runs on most systems that have Perl installed. Autodecay can be obtained from Eriksson's software web page from http://www.bergianska.se/index_forskning_soft.html.

AxParafit
type: NamedIndividual
type: Biogeographic Analysis Program

BAli-Phy
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: BI
has phylogenetic method: Bayesian Markov Chain Monte Carlo

BAMBE
type: NamedIndividual
type: General purpose packages program

BayesPhylogenies
type: NamedIndividual
type: General purpose packages program
has evolutionary model: GTR

BayesTraits
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: ML

BEAST
type: NamedIndividual
type: General purpose packages program
has evolutionary model: WAG
has evolutionary model: GTR
has evolutionary model: HKY
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: Bayesian Markov Chain Monte Carlo

BEST
type: NamedIndividual
type: Bayesian Program
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ

Bio::Phylo
type: NamedIndividual
type: General purpose packages program
description: Rutger Vos of the School of Biological Sciences of the University of Reading, United Kingdom (rutgeraldo (at) gmail.com) has released Bio::Phylo (Phyloinformatic analysis using perl), version 0.35, a phylogeny package with tree simulation, topology, visualization, data conversion functionality. It has modules for simulating tree shapes under various models, compute various tree topology indices, manage and convert data in various formats and visualize tree shapes. It is described in the paper: Vos, R. A., J. Caravas, K. Hartmann, M. A. Jensen and C. Miller. 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12: 63. http://dx.doi.org/10.1186/1471-2105-12-63. It is available as Perl script. It can be downloaded from its web site at http://search.cpan.org/dist/Bio-Phylo/

Bio++
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: ML
has phylogenetic method: Likelihood
description: Julien Y. Dutheil, Bastien Boussau, and co-workers of the Institut des Sciences de l'Evolution de Montpellier (ISE-M) of the Universit?© Montpellier 2, France (julien.dutheil (at) univ-montp2.fr) have released Bio++ version 1.8, a set of C++ libraries and programs dedicated to sequence analysis, phylogenetics, molecular evolution and population genetics. The Bio++ project is a collaborative effort to provide reusable implementations of standard phylogenetics and population genetics methods published in the literature, in order to analyze and manipulate sequence data, and with the goal to facilitate the development of new methods. Bio++ is fully object-oriented and documented. Two discussion forums are also available. A non-exhaustive list of available methods includes: sequence and tree manipulations a large set of substitution models (nucleotides, protein, codons) distance estimation and tree reconstruction (by Neighbor Joining, BIONJ and UPGMA) maximum likelihood methods nucleotide diversity estimators tools for drawing phylogenies Two recent additions also allow you to query sequences from databases and to build GUIs using the Qt libraries. A set of example programs (The Bio++ Program Suite) is also available with examples and a manual. Bio++ contains one of the largest set of models for phylogenetics, including non-homogeneous models. It also features a very general way to set up your own non-homogeneous model and fit it, for instance assuming a different equilibrium GC content for distinct clades in the phylogeny. Bio++ is distributed as source code on a CVS/SVN server, and stable snapshots are made every six months. In addition to the source code, these stable releases can also be installed as pre-compiled packages for various linux distributions. It is described in the papers: Dutheil, J., S. Gaillard, E. Bazin, S. Gl?©min, V. Ranwez, N. Galtier, and K. Belkhir. 2006. Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and …

BioEdit
type: NamedIndividual
type: Sequence Management Program

Bioinformatics_Toolbox
type: NamedIndividual
type: General purpose packages program

BIONJ
type: NamedIndividual
type: Neighbor-Joining Distance-Based Program
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ

Bionumerics
type: NamedIndividual
type: General purpose packages program
description: Applied Maths NV of Keistraat 120, 9830 Sint-Martens-Latem, Belgium (info @ applied-maths.com) has released Bionumerics, a program to manage a wide variety of biological data from 1D patterns 2D gels phenotype arrays and DNA/protein sequences. In addition to database and image processing capabilities it can do clustering and phylogenetic inference. A variety of clustering methods including UPGMA and neighbor-joining distance matrix methods are available and for inferring phylogenies generalized parsimony and maximum likelihood are described as available. Bootstrap support for groups can also be computed. There are also facilities for plotting the trees. Bionumerics is distributed as Windows executables. Bionumerics is commercial software. Information about it is available at its web site at http://www.applied-maths.com/bn/bn.htm including requesting a free demo version. For price and ordering information contact them through the web site or by email or by phone at +32 9 2222 100 fax them at +32 9 2222 102. Their U.S. Sales Office is at Applied Maths Inc. 13809 Research Blvd Suite 645 Austin Texas 78750. phone +1 512-482-9700 fax +1 512-482-9708 (email is info-us @ applied-maths.com).""

BIRCH
type: NamedIndividual
type: General purpose packages program

bms_runner
type: NamedIndividual
type: General purpose packages program

Bn-Bs
type: NamedIndividual
type: Other Disances-based Program

BootPHYML
type: NamedIndividual
type: General purpose packages program

Bosque
type: NamedIndividual
type: General purpose packages program

BPAnalysis
type: NamedIndividual
type: General purpose packages program

BRANCHLENGTH
type: NamedIndividual
type: General purpose packages program

Brownie
type: NamedIndividual
type: Clocks Dating Stratigraphy Program

burntrees
type: NamedIndividual
type: General purpose packages program

Cactus-Pie
type: NamedIndividual
type: Clocks Dating Stratigraphy Program

Cadence
type: NamedIndividual
type: General purpose packages program

CAFCA
type: NamedIndividual
type: Maximum Parsimony Program
description: Rino Zandee (rino.zandee (at) gmail.com) formerly of the Institute of Evolutionary and Ecological Science, Van der Klaauw Laboratory, Leiden University, has written CAFCA version 1.5.12, the Collection of APL Functions for Comparative Analysis. It carries out a search for the most parsimonious tree with discrete-character data (either two-state or multistate), using a search for cliques of component compatibility (monothetic subsets) to propose the candidates for most parsimonious trees. The program is written as functions in the APL language, but PowerPC Mac OS (or maybe it's Mac OS X) executables are distributed. The program is free and is available from the CAFCA Web Site at http://www.mzandee.net/~zandee/cafca/.

CAIC
type: NamedIndividual
type: Comparative Method Analysis Program

CBCAnalyzer
type: NamedIndividual
type: Neighbor-Joining Distance-Based Program

cBrother
type: NamedIndividual
type: Looking For Hybridization Or Recombination Events Program

Clann
type: NamedIndividual
type: Consensus Trees Program

ClustalW
type: NamedIndividual
type: General MSA Program

CodeAxe
type: NamedIndividual
type: Maximum Likelihood Program

CodonBootstrap
type: NamedIndividual
type: Bootstrapping Program
description: John Huelsenbeck (johnh (at) berkeley.edu) of the Department of Integrative Biology, University of California, Berkeley released CodonBootstrap version 3, now distributed by Jonathan Bollback. This is a utility that will generate non-parametric bootstrap data sets from a DNA sequence file. The program re-samples codons to (1) avoid problems when analysing data under models that assume coding structure (e.g., rates partitioned by sites), or (2) when the user wishes to re-sample sites and maintain the original autocorrelation among positions within the codon. CodonBootstrap is available as a C source code that can be compiled for Unix from Jonathan Bollback's software web page at http://www.simmap.com/bollback/software.html. A Macintosh version that was formerly distributed seems not be available any more.

CodonRates
type: NamedIndividual
type: Clocks Dating Stratigraphy Program

CoMET
type: NamedIndividual
type: Maximum Likelihood Program

COMPARE
type: NamedIndividual
type: General purpose packages program

COMPONENT
type: NamedIndividual
type: General purpose packages program

Concaterpillar
type: NamedIndividual
type: General purpose packages program

CONSEL
type: NamedIndividual
type: General purpose packages program
has evolutionary model: GTR + G
has phylogenetic method: BI
has phylogenetic method: ML

CONSERVE
type: NamedIndividual
type: Comparative Method Analysis Program

CoRe-PA
type: NamedIndividual
type: Biogeographic Analysis Program

CRANN
type: NamedIndividual
type: Maximum Parsimony Program
description: Chris Creevey and James McInerney of the Bioinformatics and Pharmacogenomics Laboratory of the National University of Ireland, Maynooth (chris.creevey (at) may.ie) have released CRANN (an Irish word for tree) version 1.04 a program to detect natural selection using rates of synonymous and nonsynonymous substitutions. Crann takes FASTA format aligned nucleotide sequence files and either infers a tree using neighbor-joining based on nonsynonymous differences or allows the user to read in a tree. It reconstructs the placements of the synonymous and nonsynonymous substitutions on the tree and carries out a statistical test for an excess of nonsynonymous changes. It can also calculate synonymous and nonsynonymous differences between all pairs of sequences and can also do that in a sliding window along the sequences. It is described in the papers: Creevey C. and J. O. McInerney. 2003. CRANN: Detecting adaptive evolution in protein-coding DNA sequences. Bioinformatics 19: 1726. Creevey C. and J. O. McInerney. 2002. An algorithm for detecting directional and non-directional positive selection neutrality and negative selection in protein coding DNA sequences. Gene 300: 43-51. It is available as Windows executables Linux executables Powermac Mac OS X executables and Mac OS 9 executables. It can be downloaded from its web site at http://bioinf.may.ie/crann/""

Crux
type: NamedIndividual
type: General purpose packages program
description: Jason Evans, of Canonware.com (jasone (at) canonware.com) has released Crux version 1.2.0, a set of Python modules together with code in C, that carries out many methods in phylogeny reconstruction. It can be used to compute distances, likelihoods, and do Bayesian MCMC on phylogenies. It can also find neighbor-joining trees, manipulate trees. and computer Robinson-Foulds distances between trees. Crux is written in Cython, an extension of Python which includes some features of the C language. Evans describes Crux as particularly useful for developing scripts to automate phylogeny tasks. Installing it requires Python and a C compiler. It is available at its web site at http://www.canonware.com/Crux/

CTree
type: NamedIndividual
type: General purpose packages program

DAMBE
type: NamedIndividual
type: General purpose packages program
has evolutionary model: TN93
description: Xuhua Xia of the Department of Biology and the Center for Advanced Research in Environmental Genomics (CAREG) of the University of Ottawa, Ontario, Canada (xxia (at) uottawa.ca) has released DAMBE (Data Analysis in Molecular Biology and Evolution), version 5.0.25, a general-purpose package for DNA and protein sequence phylogenies, and also gene frequencies. It can read and convert a number of file formats, and has many features for descriptive statistics. It can compute a number of commonly-used distance matrix measures and infer phylogenies by parsimony, distance, or likelihood methods, including bootstrapping (by sites or by codons) and jackknifing. There are a number of kinds of statistical tests of trees available, and many other features. It can also display phylogenies. DAMBE includes a copy of ClustalW there is also code from PHYLIP. An interesting feature is a simple web browser that allows sequences to be fetched over the web while running DAMBE. DAMBE is described in two publications, a paper and a book: Xia, X., and Z. Xie. 2001. DAMBE: Data analysis in molecular biology and evolution. Journal of Heredity 92: 371-373, and a book: Xia, X. 2000. Data Analysis in Molecular Biology and Evolution. Kluwer Academic Publishers, Boston. DAMBE consists of Windows executables. It is available for free from its web site at http://dambe.bio.uottawa.ca/dambe.asp. DNA sequence | protein sequence | gene frequencies http://dambe.bio.uottawa.ca/dambe.asp Xuhua Xia
label: Data Analysis in Molecular Biology and Evolution

DART
type: NamedIndividual
type: General purpose packages program

Darwin
type: NamedIndividual
type: Maximum Likelihood Program
has phylogenetic method: Likelihood

DAWG
type: NamedIndividual
type: Tree Simulation Program

DendroMaker
type: NamedIndividual
type: Tree Plotting Darwing Program

DENDRON
type: NamedIndividual
type: Other Disances-based Program

DendroPy
type: NamedIndividual
type: General purpose packages program
description: Jeet Sukumaran and Mark Holder of the Department of Ecology and Evolutionary Biology of the University of Kansas, Lawrence, Kansas (jeet (at) ku.edu) have produced DendroPy version 3.6.1, phylogenetic computing library. DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, Newick, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the libary. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting ‚Äúglue‚Äù that assembles and drives such pipelines. DendroPy's component SumTrees supersedes Sukumaran's previous program bootscore. DendroPy is described in the paper: Sukumaran, J. and Mark T. Holder. 2010. DendroPy: A Python library for phylogenetic computing. Bioinformatics 26: 1569-1571. It is available as Python script. It can be downloaded from its web site at http://packages.python.org/DendroPy/

Dendroscope
type: NamedIndividual
type: Tree Plotting Darwing Program

DERANGE2
type: NamedIndividual
type: General purpose packages program

DigTree
type: NamedIndividual
type: Tree Plotting Darwing Program

DIPLOMO
type: NamedIndividual
type: Making Distances Program

DISPAN
type: NamedIndividual
type: General purpose packages program

DISTANCE
type: NamedIndividual
type: Making Distances Program
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ
has phylogenetic method: UPGMA

DISTREE
type: NamedIndividual
type: Making Distances Program

DIVA
type: NamedIndividual
type: Biogeographic Analysis Program

DIVAGE
type: NamedIndividual
type: Making Distances Program

DIVERGE
type: NamedIndividual
type: Comparative Method Analysis Program

DNA Stacks
type: NamedIndividual
type: General purpose packages program
description: Doug Eernisse of the California State University, Fullerton (DEernisse (at) fullerton.edu) has constructed DNA Stacks version 1.3.5, a Macintosh HyperCard stack that can carry out a variety of analyses on DNA sequences. It does not do phylogenies itself. It has an alignment editor, and can carry out various kinds of translation, and codon bias analysis. It can write out data sets in PAUP, Hennig86, and PHYLIP formats. It is included here because in its Support Index Blocks... menu item it is able to prepare jobs for PAUP to enable Decay Index (Support Index) analysis. It is available by World Wide Web from http://biology.fullerton.edu/deernisse/dnastacks.html.""

dnarates
type: NamedIndividual
type: Maximum Likelihood Program

DNASIS
type: NamedIndividual
type: General purpose packages program

DnaSP
type: NamedIndividual
type: Making Distances Program

DPRML
type: NamedIndividual
type: General purpose packages program

DT-ModSel
type: NamedIndividual
type: General purpose packages program

DTdraw
type: NamedIndividual
type: General purpose packages program

DTscore
type: NamedIndividual
type: Gene Duplication And Genomic Analysis

DualBrothers
type: NamedIndividual
type: Looking For Hybridization Or Recombination Events Program

EDIBLE
type: NamedIndividual
type: General purpose packages program

EEEP
type: NamedIndividual
type: General purpose packages program

ELW
type: NamedIndividual
type: Bootstrapping Program

EMBOSS
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: NJ

EREM
type: NamedIndividual
type: General purpose packages program

ETE
type: NamedIndividual
type: General purpose packages program
description: Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabald??n of the Comparative Genomics group at the Centre for Genomic Regulation (CRG), Barcelona, Spain (jhuerta (at) crg.es) has released ETE (a python Environment for Tree Exploration), version 2.0. ETE is a Python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. It provides a broad range of tree handling options, specific methods to work on phylogenetics and clustering analyses, bindings to the phylogenomic databases such as phylomeDB, advanced node annotation, interactive visualization, and a customizable tree drawing engine to create PDF tree images. It also implements methods for orthology and paralogy prediction and topological dating. It is described in the paper: Huerta-Cepas, J., J. Dopazo and T. Gabald??n. 2010. ETE: a python Environment for Tree Exploration. BMC Bioinformatics 11: 24. It is available as C source code, Windows executables Mac OS X universal executables, and a Python module. It can be downloaded from its web site at http://ete.cgenomics.org

EvolSimulator
type: NamedIndividual
type: General purpose packages program

EvolveAGene3
type: NamedIndividual
type: Tree Simulation Program

FAMD
type: NamedIndividual
type: General purpose packages program

fastDNAml
type: NamedIndividual
type: Maximum Likelihood Program

fastDNAmlRev
type: NamedIndividual
type: Maximum Likelihood Program

FastME
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: NJ

FASTML
type: NamedIndividual
type: General purpose packages program

FastTree
type: NamedIndividual
type: General purpose packages program
has evolutionary model: JTT
has evolutionary model: WAG
has evolutionary model: Jones
has evolutionary model: LG
has evolutionary model: GTR
has phylogenetic method: ML
description: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix, Molecular Biology and Evolution.

FigTree
type: NamedIndividual
type: Tree Plotting Darwing Program

FootPrinter
type: NamedIndividual
type: General purpose packages program
description: Mathieu Blanchette, of the School of Computer Science, McGill University, Montr?©al, Qu?©bec (blanchem (at) mcb.mcgill.edu), Fei Feng (fei (at) cb.mcgill.ca), of the same school, and Martin Tompa of the Department of Computer Science and Engineering at the University of Washington, Seattle (tompa (at) cs.washington.edu) have released FootPrinter 2.0, a program that uses parsimony scores to carry out phylogenetic footprinting to search for regulatory sequences in the vicinity of genes that have been sequenced in multiple species. The program looks for locations upstream of each gene which when taken together on a known phylogeny show the largest amount of conservation by having the smallest number of changes of state along the tree. The method is described in these papers: Blanchette M. and M. Tompa. 2003. FootPrinter: a program designed for phylogenetic footprinting. Nucleic Acids Research 31: 3840-3842. Blanchette M. and M. Tompa. 2002. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Research 12: 739-748. Blanchette M. B. Schwikowski and M. Tompa. Algorithms for phylogenetic footprinting. Journal of Computational Biology 9: 211-223. The program is available as C source code (including some programs from PHYLIP) from a web site at http://bio.cs.washington.edu/software/motif_discovery#Motif%20Discovery. Two web servers are available one running FootPrinter 3.01 a more recent version and one MicroFootPrinter that searches for prokaryotic sequences that are similar to your sequence and runs a FootPrinter 2.0 on that data set.""

Forest
type: NamedIndividual
type: Tree Plotting Darwing Program

FORESTER
type: NamedIndividual
type: General purpose packages program

Freqpars
type: NamedIndividual
type: Maximum Parsimony Program
description: David Swofford, of the Center for Evolutionary Genomics, Duke University, Durham, North Carolina, together with Stewart Berlocher of the Department of Entomology of the University of Illinois, Urbana, Illinois wrote Freqpars. It implements parsimony analysis based on gene frequencies. The method was described by D. L. Swofford and S. H. Berlocher in a paper in Systematic Zoology 36: 293-325, 1987. The program is available in FORTRAN 77 source code. The search for most parsimonious trees under Swofford and Berlocher's criterion is not very extensive, Swofford notes, because the individual tree evaluations are computationally difficult. The source code in FORTRAN, with documentation, has been made available (after a period of unavailability) at Swofford's PAUP web site as one of a number of companion applications.""

FSTAT
type: NamedIndividual
type: Making Distances Program

Gambit
type: NamedIndividual
type: General purpose packages program

GAME
type: NamedIndividual
type: Other Disances-based Program

GAPars
type: NamedIndividual
type: Maximum Parsimony Program
description: Dick Hwang of the Department of Genome Sciences, University of Washington (dhwang (at) u.washington.edu) has written GAPars, a program using a genetic algorithm to search for most parsimonious phylogenies. The program is written in C++ and should compile on Unix C++ compilers and on most other C++ compilers. He describes it as working rather inefficiently and "not ready for prime-time use". It can be obtained by emailing Hwang at the address above.""

GARLI
type: NamedIndividual
type: Maximum Likelihood Program
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
comment: http://molecularevolution.org/resources/activities/garli_activity
description: GARLI (Genetic Algorithm for Rapid Likelihood Inference) performs phylogenetic searches on aligned nucleotide, codon and amino acid data sets using the maximum likelihood criterion. (http://molecularevolution.org/software/phylogenetics/GARLI)

GCUA
type: NamedIndividual
type: Making Distances Program

GDA
type: NamedIndividual
type: Other Disances-based Program

GDE
type: NamedIndividual
type: Sequence Management Program

GelCompar II
type: NamedIndividual
type: Other Disances-based Program

GeneDoc
type: NamedIndividual
type: General MSA Program

Geneious
type: NamedIndividual
type: General purpose packages program
has evolutionary model: WAG
has evolutionary model: LG
has evolutionary model: HKY
has phylogenetic method: ML
has phylogenetic method: NJ

Genepop
type: NamedIndividual
type: Making Distances Program

GeneStudio Pro
type: NamedIndividual
type: Sequence Management Program

Genetix
type: NamedIndividual
type: Making Distances Program

GeneTree
type: NamedIndividual
type: Maximum Parsimony Program
has phylogenetic method: ML
description: Rod Page (r.page (at) bio.gla.ac.uk), of the Division of Environmental and Evolutionary Biology of the University of Glasgow has released GeneTree, version 1.3.0, a program that produces reconciled trees that fit a tree of gene copies to a species tree. It uses a parsimony criterion where the penalty is the number of deletions and duplications required to reconcile the gene tree with the species tree. The program is described as "preliminary". The program is described in the paper: Page R. D. M. 1998. GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 14: 819-820 and its algorithm is described in the paper: Page R. D. M. and M. A. Charleston. 1997. From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Molecular Phylogenetics and Evolution 7: 231-240. It is available as a Macintosh executable and as an executable for Windows. They are available from the GeneTree web site at http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html. A manual is also available online there.""

GenGIS
type: NamedIndividual
type: General purpose packages program

Genie
type: NamedIndividual
type: Tree Plotting Darwing Program

GenoDive
type: NamedIndividual
type: Making Distances Program

GEODIS
type: NamedIndividual
type: Biogeographic Analysis Program
description: David Posada (dposada (at) uvigo.es), of the Universidad Vigo, Spain, Keith Crandall, of the Department of Zoology, Brigham Young University, Provo, Utah (Keith_Crandall (at) byu.edu) and Alan Templeton, of the Department of Biology of Washington University, Saint Louis, Missouri (temple_a (at) biology.wustl.edu) have made available GEODIS (version 2.6). It implements Templeton's method of Nested Clade Analysis, which is intended to distinguish between historical divergence of populations and geographical separation, using the geographical distribution of haplotypes in a genealogy. GEODIS is a Java program which can run on any platform. It is described in a paper: Posada D., K. A. Crandall and A. R. Templeton. 2000. GeoDis: A program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology 9: 487-488. It is available at its web site at http://darwin.uvigo.es/software/geodis.html

GEOMETRY
type: NamedIndividual
type: Quartets Program

GeoPhyloBuilder
type: NamedIndividual
type: Tree Plotting Darwing Program

GHOSTS
type: NamedIndividual
type: General purpose packages program

gmaes
type: NamedIndividual
type: Maximum Parsimony Program
description: Naoko Takezaki, now of the Division of Genome Analysis and Genetic Research, Department of Medicine, Kagawa University, Kagawa, Japan, (takezaki (at) med.kagawa-u.ac.jp) has written gmaes, a program that estimates a gamma distribution parameter for rate variation among sites by counting the minimum number of substitutions at each site for a given tree topology. The program is distributed as generic C source code which can be compiled on any system that has a C compiler from the IUBIO archive at http://iubio.bio.indiana.edu/soft/molbio/evolve/.

GRate
type: NamedIndividual
type: Clocks Dating Stratigraphy Program

gtp
type: NamedIndividual
type: Gene Duplication And Genomic Analysis

GZ-Gamma
type: NamedIndividual
type: Maximum Likelihood Program

Hennig86
type: NamedIndividual
type: Maximum Parsimony Program
description: J. S. Farris has produced Hennig86, a fast parsimony program including branch-and-bound search for most parsimonious trees and interactive tree rearrangement. Although complete benchmarks have not been published it is said to be faster than Swofford's PAUP both are a great many times faster than the parsimony programs in PHYLIP. The program is distributed in executable object code only and costs $50, plus $5 mailing costs ($10 outside of of the U.S.). The user's name should be stated, as copies are personalized as a copy- protection measure. It is distributed by Arnold Kluge, Amphibians and Reptiles, Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109-1079, U.S.A. (akluge (at) umich.edu) and by Diana Lipscomb at George Washington University (biodl (at) gwuvm.gwu.edu). It runs on PC-compatible microcomputers with at least 512K of RAM and needs no math coprocessor or graphics monitor. It can handle up to 180 taxa and 999 characters. It was described in the paper: Farris, J.S. 1989, Hennig86: a PC-DOS program for phylogenetic analysis. Cladistics 5: 163.

HeuristicMRF2
type: NamedIndividual
type: Consensus Trees Program

HGT
type: NamedIndividual
type: Looking For Hybridization Or Recombination Events Program

HON-new
type: NamedIndividual
type: Making Distances Program

HY-PHY
type: NamedIndividual
type: General purpose packages program

HyperTree
type: NamedIndividual
type: Tree Plotting Darwing Program

IDC
type: NamedIndividual
type: Comparative Method Analysis Program

IDEA
type: NamedIndividual
type: Maximum Parsimony Program

iGTP
type: NamedIndividual
type: General purpose packages program

IMa2
type: NamedIndividual
type: General purpose packages program

indel-Seq-Gen
type: NamedIndividual
type: Tree Simulation Program

IQPNNI
type: NamedIndividual
type: Maximum Likelihood Program

Jane
type: NamedIndividual
type: Biogeographic Analysis Program

Jevtrace
type: NamedIndividual
type: Comparative Method Analysis Program

jMODELTEST
type: NamedIndividual
type: ModelGenerationProgram
has evolutionary model: MtArt
has evolutionary model: GTR + G
has evolutionary model: GTR
has evolutionary model: HKY

Kakusan4
type: NamedIndividual
type: General purpose packages program
has evolutionary model: JC
has evolutionary model: TN93
has phylogenetic method: BI
has phylogenetic method: ML

Lagrange
type: NamedIndividual
type: Biogeographic Analysis Program

laser
type: NamedIndividual
type: Tree Plotting Darwing Program

LDDist
type: NamedIndividual
type: Making Distances Program

Leaphy
type: NamedIndividual
type: Maximum Likelihood Program

LEVEL2
type: NamedIndividual
type: Quartets Program

Likewind
type: NamedIndividual
type: Looking For Hybridization Or Recombination Events Program

Lintre
type: NamedIndividual
type: General purpose packages program

LOBSTER
type: NamedIndividual
type: General MSA Program

LVB
type: NamedIndividual
type: General purpose packages program
description: Daniel Barker (db60 (at) st-andrews.ac.uk) of the University of St. Andrews, Scotland, U.K., has written LVB version 2.2, a program for inferring phylogenies using parsimony and simulated annealing. Simulated annealing is intended to allow searches for most parsimonious trees with large numbers of species. It is described as often giving good results with large matrices. Up to 16383 objects and 32766 characters may be used. Aligned nucleotide sequences with ambiguous nucleotides and/or discrete morphological characters can be used. Bootstrapping of the data is also supported. The program is currently available in ANSI C source code as a Unix tar file, and as executables for Windows, Mac OS X, and Linux. The text of a manual can also be read or downloaded from the web site. LVB is available from its Web site at http://eggg.st-andrews.ac.uk/lvb. It is also available as a Web server from the Institut Pasteur.

Mac5
type: NamedIndividual
type: Maximum Likelihood Program

MacClade
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: BI
has phylogenetic method: ML
description: MacClade is a pioneering program for interactive analysis of evolution of a variety of character types, including discrete characters and molecular sequences. It works on Macintoshes with Mac OS X, up to and including now Leopard, Mac OS X version 10.6 (and also on Mac OS). MacClade enables you to use the mouse-window interface to specify and rearrange phylogenies by hand, and watch the number of character steps and the distribution of states of a given character on the tree change as you do so. It has many other features beyond this, including ability to edit data, print out phylogenies, and even simulate the evolution of data on a tree. MacClade was written by Wayne Maddison (now of the Department of Zoology, University of British Columbia) and David Maddison of the Department of Entomology, University of Arizona. Until 2011 it was distributed commercially by Sinauer Associates of Sunderland, Massachusetts, USA. As MacClade will not function with the forthcoming Mac OS X 10.7 (Lion), the Maddisons have made it available as a free download. It is available at the MacClade web site starting with version 4.08a. It includes a manual. An much earlier and less capable Version, 2.1 (which for example cannot read nucleic acid sequences and has many fewer features for discrete characters) is also available as a Mac OS 9 executable from the EMBL and Indiana molecular biology software servers at (respectively) iubio.bio.indiana.edu, and ftp.ebi.ac.uk, in directories molbio/mac and pub/software/mac, respectively, as a BinHexed and squeezed archive, (respectively macclade-old.hqx and macclade21.hqx. A demo version of MacClade 3 that will not save or print files is also available there.

MacroCAIC
type: NamedIndividual
type: General purpose packages program

MacT
type: NamedIndividual
type: Neighbor-Joining Distance-Based Program

MacVector
type: NamedIndividual
type: Other Disances-based Program
has phylogenetic method: ML
has phylogenetic method: NJ

MAFFT
type: NamedIndividual
type: General MSA Program

MALIGN
type: NamedIndividual
type: General purpose packages program

MANTiS
type: NamedIndividual
type: Gene Duplication And Genomic Analysis

MAPPS
type: NamedIndividual
type: ModelGenerationProgram

Mavric
type: NamedIndividual
type: Tree Plotting Darwing Program

MBEToolbox
type: NamedIndividual
type: Sequence Management Program

McRate
type: NamedIndividual
type: General purpose packages program

MEGA
type: NamedIndividual
type: General purpose packages program
has evolutionary model: JC
has evolutionary model: K80
has evolutionary model: JTT
has evolutionary model: WAG
has evolutionary model: Poisson
has evolutionary model: Jones
has evolutionary model: TN93
has evolutionary model: GTR + G
has evolutionary model: GTR
has evolutionary model: HKY
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ
has phylogenetic method: UPGMA
description: MEGA (Molecular Evolutionary Genetic Analysis) is produced by Sudhir Kumar of the Center for Evolutionary Functional Genomics of the The Biodesign Institute at Arizona State University, Tempe, Arizona (s.kumar (at) asu.edu) together with Joel Dudley of the Stanford Center for Biomedical Informatics Research at Stanford University, Koichiro Tamura of Tokyo Metropolitan University and Masatoshi Nei, of Pennsylvania State University. It carries out parsimony, distance matrix and likelihood methods for molecular data (nucleic acid sequences and protein sequences). It can do boostrapping, consensus trees, and a variety of distance measures, with Neighbor-Joining, Minimum Evolution, UPGMA, and parsimony tree methods, as a well as a large variety of data editing tasks, sequence alignment using an implementation of ClustalW, tests of the molecular clock, and single-branch tests of significance of groups. MEGA4 is the current version. MEGA4 is described in the papers: Kumar, S., J. Dudley, M. Nei and K. Tamura K. 2008. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299-306. K. Tamura, J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599. It is available for free at its web site at http://www.megasoftware.net. as Windows executables, with a downloadable manual. Manual web pages are also accessible there. It can be run under Mac OS X and under Linux using Windows emulators, if you have those. In addition, MEGA 4.1 is available as a downloadable beta release. An earlier version, MEGA 1.02, is also available there as a DOS executable. It is downloadable at the MEGA site and that version's manual is also available on line at http://evolgen.biol.metro-u.ac.jp/MEGA/manual/default.html.

MESA
type: NamedIndividual
type: General purpose packages program

Mesquite
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: ML
has phylogenetic method: Likelihood
description: Wayne Maddison of the Departments of Zoology and Botany, University of British Columbia, Vancouver, Canada, and David Maddison of the Department of Entomology, University of Arizona, Tucson, together with Peter Midford, Danny Mandel, and Jeff Oliver have released Mesquite, version 2.5. The project email address is info (at) mesquiteproject.org. Mesquite is a large and varied set of modules in Java to carry out a wide variety of analyses in comparative biology. It is also intended as a framework for other developers to use to add additional functons. Some of the over 500 functions available in the project currently are: Reconstruction of ancestral states by parsimony or likelihood and display of the reconstructed states Tests of process of character evolution, including comparative methods. Simulation of character evolution (for categorical, DNA, or continuous characters) Simulation or testing of tree shapes including the effect of a character on the shape of a tree Inferences of the fit of gene trees to species trees Parametric bootstrapping (with integration with programs such as PAUP and NONA) Morphometrics (PCA, CVA, geometric morphometrics) Coalescence (simulations, other calculations) Tree comparisons and simulations (tree similarity, Markov speciation models) Search among trees using different tree rearrangement methods as well as exhaustive enumeration Cluster analysis including single linkage and UPGMA methods Trees can be displayed and manipulated Other Java modules that use Mesquite include Tree Set Viz and a Java version of PDAP. Some mesquite modules make use of PAL. Mesquite is available in Java source code and Java executables from its web page at http://mesquiteproject.org. It can run on Mac OS X, Windows, and Linux/Unix systems using recent versions of Java.

MetaPIGA
type: NamedIndividual
type: Maximum Likelihood Program

METREE
type: NamedIndividual
type: Minimum Evolution Distance-Based Program

Mgenome
type: NamedIndividual
type: Gene Duplication And Genomic Analysis

Microsat
type: NamedIndividual
type: Making Distances Program

MINSPNET
type: NamedIndividual
type: Other Disances-based Program

MixtureTree
type: NamedIndividual
type: General purpose packages program

Modelfit
type: NamedIndividual
type: General purpose packages program

ModelGenerator
type: NamedIndividual
type: General purpose packages program
has evolutionary model: JTT
has evolutionary model: Jones
has evolutionary model: GTR
has phylogenetic method: BI
has phylogenetic method: ML

ModelTest
type: NamedIndividual
type: Bootstrapping Program

Modeltest
type: NamedIndividual
type: General purpose packages program
has evolutionary model: SYM + G
has evolutionary model: GTR + G
has evolutionary model: GTR
has evolutionary model: HKY
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: NJ

MOLPHY
type: NamedIndividual
type: Maximum Likelihood Program
comment: http://www.is.titech.ac.jp/~shimo/class/doc/csm96.pdf
description: MOLPHY is a free package of programs for molecular phylogenetics based on the Maximum Likelihood (ML) method. The main program of MOLPHY is ProtML which infers evolutionary trees from Protein (amino acid) sequences.

MrAIC
type: NamedIndividual
type: General purpose packages program
has evolutionary model: GTR

MrBayes
type: NamedIndividual
type: General purpose packages program
has evolutionary model: JC
has evolutionary model: SYM + G
has evolutionary model: JTT
has evolutionary model: WAG
has evolutionary model: Poisson
has evolutionary model: Jones
has evolutionary model: LG
has evolutionary model: MtArt
has evolutionary model: GTR + G
has evolutionary model: GTR
has evolutionary model: HKY
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ
has phylogenetic method: Bayesian Markov Chain Monte Carlo
comment: http://mrbayes.net
description: MrBayes assumes prior distribution of tree topologies and uses MCMC (Markov Chain Monte Carlo) methods to search tree space and infer the posterior distribution of topologies. It reads sequence data in the NEXUS file format, and outputs posterior distribution estimates of trees and parameters.

MrBayes tree scanners
type: NamedIndividual
type: General purpose packages program

MrBayesPlugin
type: NamedIndividual
type: Bayesian Program

MrEnt
type: NamedIndividual
type: Tree Plotting Darwing Program

MrModeltest
type: NamedIndividual
type: General purpose packages program
has evolutionary model: JC
has evolutionary model: SYM + G
has evolutionary model: GTR + G
has evolutionary model: GTR
has evolutionary model: HKY
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: NJ
has phylogenetic method: Bayesian Markov Chain Monte Carlo

MrMTgui
type: NamedIndividual
type: General purpose packages program

MSA
type: NamedIndividual
type: Making Distances Program

MULTICOMP
type: NamedIndividual
type: Making Distances Program

Multidivtime
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: BI

MultiPhyl
type: NamedIndividual
type: General purpose packages program

Murka
type: NamedIndividual
type: General purpose packages program
description: Valery Zaporozhchenko of the Research Centre for Medical Genetics, Moscow, Russia (valery (at) regmed.ru) has released Murka version 1.2, a phylogeny package for parsimony methods. It constructs median networks and from them finds Steiner trees (estimates of the most parsimonious tree) from biological alignments. The package includes subprograms for building full median networks and their subsets (such as Median Joining and Reduced Median networks), extracting Steiner trees and analyzing results. Murka is a cross-platform command line application with a source code distributed under the LGPL license. Documentation can be viewed at the documentation page at its web site. It is available as C++ source code, Windows executables and Linux executables. It can be downloaded from its web site at http://phylomurka.sourceforge.net For visualization of trees and networks Murka requires that the graph visualization programs GrappViz also be installed.

MUSCLE
type: NamedIndividual
type: General MSA Program

MUST 2000
type: NamedIndividual
type: Sequence Management Program

MVSP
type: NamedIndividual
type: Other Disances-based Program

NEPAL
type: NamedIndividual
type: Maximum Likelihood Program

NetRecodon
type: NamedIndividual
type: Tree Simulation Program

Network
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: Likelihood

NHML
type: NamedIndividual
type: General purpose packages program

nhPhyML
type: NamedIndividual
type: Maximum Likelihood Program

NimbleTree
type: NamedIndividual
type: General purpose packages program

NINJA
type: NamedIndividual
type: Neighbor-Joining Distance-Based Program
comment: http://nimbletwist.com/software/ninja/docs.html
description: NINJA is a software for large-scale neighbor-joining phylogeny inference.

NJplot
type: NamedIndividual
type: Tree Plotting Darwing Program

nneighbor
type: NamedIndividual
type: Neighbor-Joining Distance-Based Program

NONA
type: NamedIndividual
type: Maximum Parsimony Program
description: Pablo Goloboff, of INSUE - Fundaci??n e Instituto Miguel Lillo 205, 4000 S. M. de Tucum?°n, Argentina (instlillo (at) infovia.com.ar with Subject line para Pablo Goloboff) has written NONA (Noname) version 2.0 PiWe (Parsimony with Implied WEights) and SPA to carry out parsimony including weighted parsimony analyses. NONA searches for most parsimonious trees according to character weights defined by the user a priori. Pee-Wee calculates weights of the characters by a method introduced by Goloboff a noniterative version of J. S. Farris's "successive weighting". It was described in Goloboff's paper in Cladistics 9: 83-91 1993. SPA is a generalized parsimony program that allows differential weighting of changes between different states. NONA is said to be faster than other parsimony programs. A Windows version of NONA which includes Piwe and SPA is available as freeware from its web page at http://www.cladistics.com/aboutNona.htm." DNA sequence | discrete characters http://www.cladistics.com/aboutNona.htm"

Notung
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: Likelihood

NSA
type: NamedIndividual
type: Making Distances Program

NTSYSpc
type: NamedIndividual
type: General purpose packages program

ODEN
type: NamedIndividual
type: Other Disances-based Program

OSA
type: NamedIndividual
type: General purpose packages program

OUCH
type: NamedIndividual
type: Comparative Method Analysis Program

p4
type: NamedIndividual
type: Bayesian Program

PAL
type: NamedIndividual
type: General purpose packages program
description: Matthew Goode, Alexei Drummond, Ed Buckler, and Korbinian Strimmer, together with seven other contributors, have released PAL (Phylogenetic Analysis Library) version 1.5, a free collection of Java classes for use in molecular phylogenetics. The addresses of the four principal contributers are respectively: Matthew Goode (m.goode (at) auckland.ac.nz), Bioinformatics Institute, School of Biological Sciences, University of Auckland, New Zealand. Alexei Drummond (alexei (at) cs.auckland.ac.nz, Department of Computer Science, University of Auckland, New Zealand Ed Buckler (esb33 (at) cornell.edu), Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York. Korbinian Strimmer (strimmer (at) uni-leipzig.de, Institute for Medical Informatics, Statistics and Epidemiology (IMISE) of the University of Leipzig, Germany. PAL is intended to facilitate the rapid construction of both general applications as well as special-purpose tools for phylogenetic analysis. It focuses on probabilistic data modelling and provides, e.g., routines for maximum likelihood, neighbor-joining and least squares analysis probability models for nucleotide/amino acid substitution, including constraints for a molecular clock bootstrapping, and the Kishino-Hasegawa-Templeton and Shimodaira-Hasegawa tests simulation of trees and data sets, including coalescent trees with growing populations and serial samples reading and write trees and alignments adjusting for rate variation among sites obtaining splits from trees and calculating a distance between trees among many other functions. It currently consists of over 200 components in 16 packages. PAL is described in a paper: Drummond, A., and K. Strimmer. 2001. PAL: An object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 17: 662-663. It is available at its web site at http://www.cebl.auckland.ac.nz/pal-project/. Two user interfaces are available which contain application programs written using PAL. T…

Paloverde
type: NamedIndividual
type: Tree Plotting Darwing Program

PAML
type: NamedIndividual
type: General purpose packages program
has evolutionary model: HKY
has phylogenetic method: ML
has phylogenetic method: NJ

ParaFit
type: NamedIndividual
type: Biogeographic Analysis Program

PARAT
type: NamedIndividual
type: Maximum Likelihood Program

PARBOOT
type: NamedIndividual
type: General purpose packages program

Parsimov
type: NamedIndividual
type: General purpose packages program
description: Jon Jeffery (jon (at) donnasaxby.com), then of the Insitute of Biology, Leiden University, The Netherlands has written Parsimov, a series of Perl scripts to implement event cracking a parsimony-based method of finding the minimum number of changes in developmental sequences of events that are necessary to explain the evolution of pairs of characters on a tree. Among the uses of this method is to reconstruct ancestral developmental sequences. The programs include: Parsimv7g.pl which implements event-pair "parsimony cracking". ReplacerParsimv.pl which takes a Parsimv7g.pl output file and replaces the PAUP character numbers with more readable character names according to a user-specified text list. Describe.pl which creates a PAUP command file to describe each tree in memory under ACCTRAN and DELTRAN optimizations (saving each as separate log files) plus a Parsimv7g.pl batch file (e.g. ParsBatch.txt) to crack each of the PAUP log files produced. The programs can be executed on any system that has Perl installed. They are described in a paper: Jeffery J.E. O.R.P. Bininda-Emonds M.I. Coates and M.K. Richardson. 2005. A new technique for identifying sequence heterochrony. Systematic Biology 54: 230-240. The Parsimov programs are available as (separate) downloads at Olaf Bininda-Emonds's software web page at http://www.uni-oldenburg.de/molekularesystematik/en/34011.html#EvoDevo""

partimatrix
type: NamedIndividual
type: Looking For Hybridization Or Recombination Events Program

PASSML
type: NamedIndividual
type: Maximum Likelihood Program

PAST
type: NamedIndividual
type: General purpose packages program

PATHd8
type: NamedIndividual
type: Clocks Dating Stratigraphy Program

PAUP
type: NamedIndividual
type: General purpose packages program
has evolutionary model: K80
has evolutionary model: SYM + G
has evolutionary model: GTR + G
has evolutionary model: GTR
has evolutionary model: HKY
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ
comment: http://www.sinauer.com/detail.php
description: David Swofford of the School of Computational Science and Information Technology, Florida State University, Tallahassee, Florida has written PAUP (which originally meant Phylogenetic Analysis Using Parsimony). PAUP version 4.0beta10 has been released as a provisional version by Sinauer Associates, of Sunderland, Massachusetts. It has Macintosh, PowerMac, Windows, and Unix/OpenVMS versions. PAUP has many options and close compatibility with MacClade. It includes parsimony, distance matrix, invariants, and maximum likelihood methods and many indices and statistical tests. It is described in a web page at http://paup.csit.fsu.edu/, which also contains links to its web pages at Sinauer Associates. It is available for the following types of systems: For PowerMac and 68k Macintosh Mac OS 9 in a version with full mouse-windows user interface, which can also be run under the Classic environment on Mac OS X, For PowerPC Mac OS X systems or Intel Mac OS X systems when running under emulation) in a version with a command-line interface, For Windows in a version with a character-based command-line interface (which appears in a Windows window), For DOS or a Windows DOS box in a version which has command-line interface, and In a Unix/Linux version, with command-line interface, for Alpha Compaq/Digital Unix, Alpha Linux, PowerPC Linux, Intel-compatible Linux, Sun SPARC/UltraSPARC Solaris, and Alpha VMS. The price is $100 US for the Macintosh and PowerMac executable versions, $85 for the Windows executable version, and $150 for the Unix source code version, plus $20 for shipment. The Beta version comes with a Command Reference Document. Their ISBN numbers are 0-87893-806-0, -807-9, and -804-4. Contact and ordering information will be found at the Sinauer Associates web site. The international distributor for many countries is Palgrave Macmillan, Brunel Road, Houndsmills, Basingstoke, Hampshire RG21 6XS, U.K. Tel: +44-1256-329242 Fax: +44-1256-330688. Their e-mail address is lecture…

PAUPRat
type: NamedIndividual
type: Maximum Likelihood Program
has phylogenetic method: Likelihood

PaupUp
type: NamedIndividual
type: General purpose packages program
description: Fr?©d?©ric Calendini and Jean-Francois Martin of the Departement Protection des plantes et environnment of the Ecole Nationale Sup?©rieur, Montpellier, France (martinjf (at) ensam.inra.fr) have produced PaupUp version 1.0.3.1, a graphical frontend for Paup DOS software. The PauUp program provides a user-friendly interface to the phylogenetic program PAUP on the Windows operating systems. The DOS version of PAUP is entirely command-line driven and does not provide any graphical interface. PaupUp partly resolves this issue, providing around 80% of the available commands (the most commonly used in our opinion) in a graphical environment comparable to the MAC OS version while the last 20% commands are still available through direct command-line input in a single integrated design. The programs TreeView and Modeltest can be called from PaupUp. PaupUp is not compatible with the Windows version of PAUP but is compatible with the DOS version that is distributed with that Windows version. It is available as a Windows executable. It also requires the Microsoft .NET executable framework to be installed. PaupUp can be downloaded from its web site at http://www.agro-montpellier.fr/sppe/Recherche/JFM/PaupUp/

PC-ORD
type: NamedIndividual
type: ClusterAnalysisDistanceBasedProgram

pcca
type: NamedIndividual
type: Comparative Method Analysis Program

PDAP
type: NamedIndividual
type: General purpose packages program

PEBBLE
type: NamedIndividual
type: General purpose packages program

Permute!
type: NamedIndividual
type: General purpose packages program

phangorn
type: NamedIndividual
type: General purpose packages program

PHASE
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: ML

Phybase
type: NamedIndividual
type: General purpose packages program

PHYDIT
type: NamedIndividual
type: Sequence Management Program

Phyledit
type: NamedIndividual
type: Sequence Management Program

PHYLIP
type: NamedIndividual
type: General purpose packages program
has evolutionary model: K80
has evolutionary model: JTT
has evolutionary model: WAG
has evolutionary model: Poisson
has evolutionary model: Jones
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ
has phylogenetic method: UPGMA
comment: http://evolution.gs.washington.edu/phylip.html
description: PHYLIP version 3.6 is my own package. It is available free, from its Web site, in C source code, or as executables for Windows, Mac OS X, and Mac OS 8 or 9. The C source code can easily be compiled on Unix or Linux systems. It includes programs to carry out parsimony, distance matrix methods, maximum likelihood, and other methods on a variety of types of data, including DNA and RNA sequences, protein sequences, restriction sites, 0/1 discrete characters data, gene frequencies, continuous characters and distance matrices. It may be the most widely-distributed phylogeny package, with about 29,000 registered users, some of them satisfied. It is third after PAUP and MrBayes in the competition to be the program responsible for the most published trees. It has been distributed since October, 1980 and has celebrated its 30th anniversary, as the oldest distributed phylogeny package. PHYLIP is distributed at the PHYLIP web site at http://evolution.gs.washington.edu/phylip.html. A number of sites offer web-servers that will perform data analyses using PHYLIP.

PHYLLAB
type: NamedIndividual
type: General purpose packages program

Phylo_win
type: NamedIndividual
type: General purpose packages program

PhyloBayes
type: NamedIndividual
type: General purpose packages program
has evolutionary model: WAG
has evolutionary model: Poisson
has evolutionary model: LG
has evolutionary model: GTR
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Bayesian Markov Chain Monte Carlo

PhyloCoCo
type: NamedIndividual
type: Maximum Likelihood Program

Phylocom
type: NamedIndividual
type: General purpose packages program

Phylodendron
type: NamedIndividual
type: Tree Plotting Darwing Program

Phylogen
type: NamedIndividual
type: Tree Simulation Program

Phylogenetic Independence
type: NamedIndividual
type: Comparative Method Analysis Program

Phylogenetic Tree Drawing
type: NamedIndividual
type: Tree Plotting Darwing Program

PHYLOGR
type: NamedIndividual
type: Comparative Method Analysis Program

PhyloNet
type: NamedIndividual
type: General purpose packages program

PhyloQuart
type: NamedIndividual
type: Quartets Program

PhyloSort
type: NamedIndividual
type: Consensus Trees Program

PhyloWidget
type: NamedIndividual
type: Tree Plotting Darwing Program

PHYLTEST
type: NamedIndividual
type: General purpose packages program

Phyltools
type: NamedIndividual
type: General purpose packages program

PHYML
type: NamedIndividual
type: General purpose packages program
has evolutionary model: JTT
has evolutionary model: WAG
has evolutionary model: Jones
has evolutionary model: LG
has evolutionary model: MtArt
has evolutionary model: TN93
has evolutionary model: GTR + G
has evolutionary model: GTR
has evolutionary model: HKY
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ
has phylogenetic method: Bayesian Markov Chain Monte Carlo

PhyML-Multi
type: NamedIndividual
type: General purpose packages program

PhyNav
type: NamedIndividual
type: General purpose packages program

PhyRe
type: NamedIndividual
type: Tree Plotting Darwing Program

PhySIC_IST
type: NamedIndividual
type: Consensus Trees Program

PHYSIG
type: NamedIndividual
type: General purpose packages program

Phyutility
type: NamedIndividual
type: General purpose packages program

PICA
type: NamedIndividual
type: General purpose packages program

PISE
type: NamedIndividual
type: Sequence Management Program

PLATO
type: NamedIndividual
type: General purpose packages program

POPGENE
type: NamedIndividual
type: Making Distances Program

POPTREE2
type: NamedIndividual
type: General purpose packages program

Populations
type: NamedIndividual
type: General purpose packages program

Porn
type: NamedIndividual
type: General purpose packages program

POY
type: NamedIndividual
type: General purpose packages program
description: POY is a program for phylogenetic analysis of DNA sequence data based on the principle behavior of parsimony. POY uses concepts of homology of DNA sequence data than those of static DNA sequence alignments. This program implements two methods of DNA analysis ‚ optimization alignment‚Äù and ‚Äúfixed-states optimization‚Äù.Exploring the Behavior of POY, a Program for Direct Optimization of Molecular Data, Cladistics 17, S60‚ÄìS70 (2001)

PPH
type: NamedIndividual
type: Looking For Hybridization Or Recombination Events Program

PRAP
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: Likelihood
description: Kai M?ºller of the Nees-Institut f?ºr Biodiversit&aauml t der Pflanzen of the University of Bonn, Germany (kaimueller (at) uni-bonn.de) has written PRAP (Parsimony Ratchet Analyses using PAUP and likelihood) version 2.0, a Java program to drive PAUP in computing Bremer support of groups, and in doing ratchet searches for parsimony or likelihood trees. It allows the user to make PAUP carry out searches using the parsimony ratchet strategy of Kevin Nixon. In version 2.0 this can be done using either the parsimony criterion or the likelihood criterion (in spite of the name of the search method). It can also do variations on the parsimony ratchet including multiple random addition sequences. It is described in the paper: M?ºller K. F. 2004. PRAP - computation of Bremer support for large data sets. Molecular Phylogenetics and Evolution 31: 780-782 and the search strategies it implements are described in the paper: M?ºller K. 2005. The efficiency of different search strategies in estimating parsimony jackknife bootstrap and Bremer support. BMC Evolutionary Biology 5: 58. It is available as Java executables as downloads for Windows Mac OS X and for Unix. It can be downloaded from its web site at http://systevol.nees.uni-bonn.de/software. The earlier versions 1.0 and 0.99 are also available there.""

PROCOV
type: NamedIndividual
type: Maximum Likelihood Program

ProfDist
type: NamedIndividual
type: Neighbor-Joining Distance-Based Program

ProSeq
type: NamedIndividual
type: Tree Simulation Program

ProtTest
type: NamedIndividual
type: General purpose packages program
has evolutionary model: JTT
has evolutionary model: WAG
has evolutionary model: Jones
has evolutionary model: LG
has evolutionary model: MtArt
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: NJ
has phylogenetic method: Bayesian Markov Chain Monte Carlo

PSeq-Gen
type: NamedIndividual
type: Tree Simulation Program

PSODA
type: NamedIndividual
type: Maximum Parsimony Program
description: Quinn Snell, Mark Clement, and Hyrum Carroll of the Computational Science Laboratory of the Department of Computer Science at Brigham Young University, Provo, Utah (snell (at) cs.byu.edu) and (clement (at) cs.byu.edu) have written PSODA, a parsimony program for nucleotide sequences. The program reads the NEXUS file format, and carries out heuristic rearrangement of trees using the parsimony criterion. It is available as C++ source code, Windows executables, Linux executables and Powermac Mac OS X executables. It can be downloaded from its web site at http://dna.cs.byu.edu/psoda/

PTP
type: NamedIndividual
type: Maximum Likelihood Program
has phylogenetic method: ML

puzzleboot
type: NamedIndividual
type: General purpose packages program

PyCogent
type: NamedIndividual
type: Sequence Management Program
description: Gavin Huttley, Rob Knight, PyCogent Development Team of the John Curtin School of Medical Research of the Australian National University, Canberra, Australia (gavin.huttley (at) anu.edu.au) has released PyCogent (COmparative GENomics Toolkit, written in Python)), version 1.4.1. PyCogent is a software library for genomic biology. It is an integrated framework for controlling third-party applications devising workflows querying databases conducting novel probabilistic analyses of biological sequence evolution and generating publication quality graphics. It is intended that it be able to carry out a variety of phylogeny methods itself, but for now these have not been implemented. It can, however, be used to submit runs of some existing programs to infer phylogenies, including RAxML, FASTML, and Muscle. It is described in the paper: Knight, R., P. Maxwell, A. Birmingham, J. Carnes, J. G. Caporaso, B. C. Easton et al. 2007. Pycogent: A toolkit for making sense from sequence. Genome Biology 8(8): R171. It is available as C source code, Python script, Linux executables, Intel Mac OS X executables and Mac OS X universal executables. It can be downloaded from its web site at http://pycogent.sourceforge.net/

qclust
type: NamedIndividual
type: Neighbor-Joining Distance-Based Program

QDate
type: NamedIndividual
type: Clocks Dating Stratigraphy Program

Quartet Suite
type: NamedIndividual
type: General purpose packages program

QuickTree
type: NamedIndividual
type: Neighbor-Joining Distance-Based Program

r8s
type: NamedIndividual
type: Clocks Dating Stratigraphy Program

r8s-bootstrap
type: NamedIndividual
type: General purpose packages program

RA
type: NamedIndividual
type: Maximum Parsimony Program
has phylogenetic method: ML
has phylogenetic method: Likelihood
description: J. S. Farris has written RA (Rapid nucleotide Analysis). It features rapid bootstrapping. It is available from Arnold Kluge, Amphibians and Reptiles, Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109-1079, U.S.A. (akluge (at) umich.edu) and Diana Lipscomb at George Washington University (BIODL (at) gwuvm.gwu.edu) who may be contacted for details. The cost is said to be about $30 US.

RadCon
type: NamedIndividual
type: General purpose packages program

Rainbow
type: NamedIndividual
type: Consensus Trees Program

Random Cladistics
type: NamedIndividual
type: General purpose packages program
description: Mark Siddall, Assistant Curator of Annelida at the American Museum of Natural History, New York (siddall (at) amnh.org) has released Random Cladistics, version 4.0.3, a set of programs that can carry out bootstrapping, jackknifing, a variety of kinds of permutation tests, and search for islands of trees using Hennig86 or NONA to analyze the data. It can also mark ranges of sites for inclusion or exclusion compare trees from the analyses compute an index of incongruence between data sets and do many other operations. To use it you must have a copy of Hennig86 (for whose distribution see above). Random Cladistics will carry out the appropriate transformations of your data and will call Hennig86 and have it analyze them and then it will summarize the results. Random Cladistics is described by its author as no longer being supported software -- he says that "Winclada is far superior and provide's a nice interface." Random Cladistics and associated programs are still distributed by their author from its web site at http://research.amnh.org/~siddall/rc.html as MSDOS executables.""

RAPDistance
type: NamedIndividual
type: Making Distances Program

rate-evolution
type: NamedIndividual
type: General purpose packages program

Rate4Site
type: NamedIndividual
type: Maximum Likelihood Program
has phylogenetic method: ML

RAxML
type: NamedIndividual
type: General purpose packages program
has evolutionary model: JTT
has evolutionary model: WAG
has evolutionary model: LG
has evolutionary model: GTR + G
has evolutionary model: GTR
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ
description: It is a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method. It provides faster heuristic search, use of parallel processing, and a simulated annealing algorithm. Molecular sequence data RAxML-II: a program for sequential, parallel and distributed inference of large phylogenetic trees, Concurrency Computat.: Pract. Exper. 2005 17:1705‚Äì1723.

raxmlGUI
type: NamedIndividual
type: General purpose packages program
has evolutionary model: GTR
has phylogenetic method: BI
has phylogenetic method: ML

RDP3
type: NamedIndividual
type: Looking For Hybridization Or Recombination Events Program

REAP
type: NamedIndividual
type: Making Distances Program

Recodon
type: NamedIndividual
type: Tree Simulation Program

RecPars
type: NamedIndividual
type: Looking For Hybridization Or Recombination Events Program

REDCON
type: NamedIndividual
type: Consensus Trees Program

RESTSITE
type: NamedIndividual
type: Other Disances-based Program

RevDNArates
type: NamedIndividual
type: Maximum Likelihood Program

Rhino
type: NamedIndividual
type: General purpose packages program

RIND
type: NamedIndividual
type: Comparative Method Analysis Program

Robinson and Foulds distance
type: NamedIndividual
type: Consensus Trees Program

ROSE
type: NamedIndividual
type: Tree Simulation Program

rRNA phylogeny
type: NamedIndividual
type: Maximum Likelihood Program
has phylogenetic method: NJ

RRTree
type: NamedIndividual
type: Clocks Dating Stratigraphy Program

RSTCALC
type: NamedIndividual
type: Making Distances Program

S-DIVA
type: NamedIndividual
type: General purpose packages program

scaleboot
type: NamedIndividual
type: Bootstrapping Program

SeaView
type: NamedIndividual
type: General purpose packages program
has evolutionary model: K80
has evolutionary model: WAG
has evolutionary model: LG
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ

Segminator
type: NamedIndividual
type: General purpose packages program

SEMPHY
type: NamedIndividual
type: Maximum Likelihood Program

sendbs
type: NamedIndividual
type: Neighbor-Joining Distance-Based Program

Seq-Gen
type: NamedIndividual
type: Tree Simulation Program

SeqPup
type: NamedIndividual
type: General purpose packages program

SeqState
type: NamedIndividual
type: Maximum Likelihood Program
description: Kai M?ºller of the Nees-Institut f?ºr Biodiversit?§t der Pflanzen of the University of Bonn, Germany (kaimueller (at) uni-bonn.de) has produced SeqState version 1.40. It carries out a variety of primer design functions and also calculates various statistics on aligned DNA sequences. For the purposes of this listing, the relevant feature is that it can be used to implement a number of different kinds of coding of indels (insertions and deletions). It is described in the paper: M?ºller K. F. 2005. SeqState - primer design and sequence statistics for phylogenetic DNA data sets. Applied Bioinformatics 4: 65-69 and the different indel coding methods are discussed in two other papers: M?ºller, K. F. 2006. Incorporating information from length-mutational events into phylogenetic analysis. Molecular Phylogenetics and Evolution 38: 667-676. Simmons, M. P., K. F. M?ºller, A. P. Norton. 2007. The relative performance of indel-coding methods in simulations. Molecular Phylogenetics and Evolution 44: 724-740. It is available as Java executables, for Windows, for Mac OS X, and for Linux. It can be downloaded from its web site at http://systevol.nees.uni-bonn.de/software/SeqState

SGRunner
type: NamedIndividual
type: Tree Simulation Program

SIMMAP
type: NamedIndividual
type: General purpose packages program

SimpleClade
type: NamedIndividual
type: Tree Plotting Darwing Program

Simplot
type: NamedIndividual
type: General purpose packages program
has evolutionary model: K80
has phylogenetic method: NJ

Simprot
type: NamedIndividual
type: Tree Simulation Program

Singapore PHYLIP web interface
type: NamedIndividual
type: Sequence Management Program

SLOUCH
type: NamedIndividual
type: Comparative Method Analysis Program

SLR
type: NamedIndividual
type: Maximum Likelihood Program

sog
type: NamedIndividual
type: General purpose packages program
description: John Czelusniak, then of the Department of Anatomy and Cell Biology, Wayne State University, Detroit, Michigan wrote sog, a C program demonstrating an algorithm to find the most parsimonious phylogeny along with the parsimony strength of grouping (or Bremer decay index) for nucleotide sequences in one pass of a branch and bound algorithm. This differs from the implementation in PAUP which uses a separate branch and bound search to find the strength of grouping for each group in the tree, using the tree group exclusion option. John said (some time ago) that sog is a rather ugly hack which will be optimized and streamlined. It IS ALPHA SOFTWARE which means it has not been tested extensively on datasets other than our primate datasets. It is available at the IUBIO archive at http://iubio.bio.indiana.edu/soft/molbio/evolve/. It is distributed as generic C source code which should be able to compile and run on any system that has a C compiler.""

SPAGeDi
type: NamedIndividual
type: Making Distances Program

Spectronet
type: NamedIndividual
type: General purpose packages program

Spectrum
type: NamedIndividual
type: Maximum Likelihood Program

SplitsTree
type: NamedIndividual
type: Maximum Likelihood Program

SSA
type: NamedIndividual
type: Maximum Likelihood Program

START2
type: NamedIndividual
type: General purpose packages program

Statio
type: NamedIndividual
type: General purpose packages program

STC
type: NamedIndividual
type: ClusterAnalysisDistanceBasedProgram

SuiteMSA
type: NamedIndividual
type: General purpose packages program

SuperTree
type: NamedIndividual
type: Consensus Trees Program

Supertree scripts
type: NamedIndividual
type: Consensus Trees Program

Swaap
type: NamedIndividual
type: Making Distances Program

Swaap PH
type: NamedIndividual
type: Making Distances Program

SWORDS
type: NamedIndividual
type: General purpose packages program

SymmeTREE
type: NamedIndividual
type: General purpose packages program

SYN-TAX
type: NamedIndividual
type: ClusterAnalysisDistanceBasedProgram

T-Coffee
type: NamedIndividual
type: General MSA Program

T-REX
type: NamedIndividual
type: General purpose packages program

Tarzan
type: NamedIndividual
type: Biogeographic Analysis Program

TAXEQ3
type: NamedIndividual
type: Bootstrapping Program

TCS
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: Likelihood
description: Mark Clement, David Posada, and Keith Crandall of the Universidad Vigo, Spain (Posada) and the Department of Zoology, Brigham Young University, Provo, Utah (dposada (at) uvigo.es) have released TCS version 1.21, a program for estimating gene genealogies within a population. It does so by using the method introduced in the paper: Templeton, A. R., K. A. Crandall and C. F. Sing. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132: 619-633. This is a method that connects existing haplotypes in a minimum spanning tree which is essentially a parsimony method. It can also infer networks with loops in them. TCS is written in Java and has a graphic user interface for the display of the resulting networks. It may be run on any system that has the Java runtime environment. The program is described in the paper: Clement M., D. Posada, and K. Crandall. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1660. It implements the estimation of the 95% parsimony connection limit, and the estimation of outgroup weights (which are used to designate the root of the tree). It takes as input sequence files in NEXUS or PHYLIP format, and accepts absolute distances between sequences as input. The output is a Postscript picture of the tree, which can be saved as a Postscript file. TCS is available as Java executables, with documentation, at its web site at http://darwin.uvigo.es/software/tcs.html.

TFPGA
type: NamedIndividual
type: Making Distances Program

TIMER
type: NamedIndividual
type: General purpose packages program

TipDate
type: NamedIndividual
type: General purpose packages program

TNT
type: NamedIndividual
type: Maximum Parsimony Program
has phylogenetic method: ML
has phylogenetic method: Likelihood
description: Pablo Goloboff, of INSUE - Fundaci??n e Instituto Miguel Lillo 205, 4000 S. M. de Tucum?°n, Argentina, (pablogolo (at) csnat.unt.edu.ar) together with J. S. Farris of the, Laboratory of Molecular Systematics of the Naturhistoriska Riksmuseet, Stockholm, Sweden and Kevin Nixon of the L. H. Bailey Hortorium, Cornell University, Ithaca, New York, have produced TNT (Tree analysis using New Technology), version of August 2008. This is a parsimony program intended for use on very large data sets. It makes use of the methods for speeding up parsimony searches introduced by Goloboff in the paper: Goloboff, P.A. 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15: 415-428, and the highly effective parsimony ratchet search strategy introduced by Nixon in the paper: Nixon K.C. 1999. The parsimony ratchet a new method for rapid parsimony analysis. Cladistics 15: 407-414. It can handle characters with discrete states as well as continuous characters. The program is distributed as Windows Linux and both PowerMac and Intel Mac OS X executables. The program and some support files including documentation is available from its web page at http://www.zmuc.dk/public/phylogeny/TNT It is free provided you agree to a license with some reasonable limitations.""

TOPALi
type: NamedIndividual
type: General purpose packages program
has evolutionary model: SYM
has evolutionary model: JTT
has evolutionary model: GTR + G
has evolutionary model: GTR
has phylogenetic method: ML

TopD/fMts
type: NamedIndividual
type: General purpose packages program

tracer
type: NamedIndividual
type: General purpose packages program
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: Bayesian Markov Chain Monte Carlo

Tracer
type: NamedIndividual
type: Tree Plotting Darwing Program

Tree Draw Deck
type: NamedIndividual
type: Tree Plotting Darwing Program

Tree Tracker
type: NamedIndividual
type: Gene Duplication And Genomic Analysis

TREE-PUZZLE
type: NamedIndividual
type: Maximum Likelihood Program
has phylogenetic method: ML
has phylogenetic method: NJ
comment: http://www.tree-puzzle.de/
description: This is a program for tree estimation and to reconstruct phylogenetic trees. It implements a fast tree search algorithm by the strategy of ‚Äúquartet puzzling‚Äù which allows large data sets. It also computes pair-wise maximum likelihood distances as well as branch lengths for user specified trees. It also conducts a number of statistical tests on the data sets.

TreeAlign
type: NamedIndividual
type: General MSA Program

TREECON
type: NamedIndividual
type: General purpose packages program
has evolutionary model: Poisson

TreeDis
type: NamedIndividual
type: Comparative Method Analysis Program

TreeDyn
type: NamedIndividual
type: Tree Plotting Darwing Program

TreeEdit
type: NamedIndividual
type: General purpose packages program

TreeExplorer
type: NamedIndividual
type: Tree Plotting Darwing Program

Treefinder
type: NamedIndividual
type: General purpose packages program
has evolutionary model: WAG
has evolutionary model: MtArt
has evolutionary model: GTR
has evolutionary model: HKY
has phylogenetic method: BI
has phylogenetic method: ML
has phylogenetic method: NJ

TreeFit
type: NamedIndividual
type: General purpose packages program

TreeFitter
type: NamedIndividual
type: Biogeographic Analysis Program

TreeGraph 2
type: NamedIndividual
type: Tree Plotting Darwing Program

TreeJuxtaposer
type: NamedIndividual
type: Tree Plotting Darwing Program

TreeMaker
type: NamedIndividual
type: Tree Plotting Darwing Program

TREEMAP
type: NamedIndividual
type: General purpose packages program

TreeMe
type: NamedIndividual
type: Tree Plotting Darwing Program

TreeRot
type: NamedIndividual
type: Bootstrapping Program
description: Michael Sorenson of the Department of Biology, Boston University (msoren (at) bu.edu) has released TreeRot, version 3, a program that helps make Bremer Support Indices (decay indices) for parsimony analyses. It generates a PAUP command file with a constraint statement for each node in a given shortest or strict consensus tree and with commands to search for trees inconsistent with each of these constraint statements in turn. For nodes with decay indices of more than a few steps the constraint statement approach is much more effective than simply finding all trees 1 2 3 4 etc. steps longer than the shortest tree and then examining their strict consensus for which nodes are lost. This version also supports the determination of partitioned Bremer support indices introduced in the paper: Baker R.H. and R. DeSalle. 1997. Multiple sources of character information and the phylogeny of Hawaiian Drosophilids. Systematic Biology 46: 654-673 and it will also parse the PAUP log file automatically calculating the decay index for each node. It is written in the Perl scripting language and a Mac OS Macintosh executable is also available. Both are distributed at its web site at http://people.bu.edu/msoren/TreeRot.html.""

TreeSAAP
type: NamedIndividual
type: Comparative Method Analysis Program

TreeScan
type: NamedIndividual
type: Tree Plotting Darwing Program

TreeSetViz
type: NamedIndividual
type: Tree Plotting Darwing Program

TreeSnatcher Plus
type: NamedIndividual
type: Tree Plotting Darwing Program

TreeStat
type: NamedIndividual
type: Tree Plotting Darwing Program

TreeThief
type: NamedIndividual
type: Tree Plotting Darwing Program

TreeTool
type: NamedIndividual
type: Tree Plotting Darwing Program

TreeToy
type: NamedIndividual
type: Tree Plotting Darwing Program

TreeView
type: NamedIndividual
type: Tree Plotting Darwing Program

Treevolve and PTreevolve
type: NamedIndividual
type: Tree Simulation Program

UGENE
type: NamedIndividual
type: General purpose packages program

unrooted
type: NamedIndividual
type: Tree Plotting Darwing Program

Vanilla
type: NamedIndividual
type: General purpose packages program
description: Korbinian Strimmer, of the Institute for Medical Informatics, Statistics and Epidemiology (IMISE) of the University of Leipzig, Germany (strimmer (at) uni-leipzig.de), has written Vanilla, version 1.2, a character-based interface to the PAL Java classes, which includes a number of programs carrying out different kinds of phylogenetic analysis, including: MLDIST which computes maximum likelihood distances between DNA sequences, protein sequences, and two-state data, with correction for unequal rates at different sites. It has many different substitution models available. It also computes observed distances and can obtain approximate estimates of unknown model parameters such as the Ts/Tv ratio. MLTREE which computes the likelihood of a given tree under the same models as MLDIST, allowing branch lengths to be provided or to be estimated by the program, with the possibility of constraining them to be clocklike. If two or more tree are provided it can also compare them using the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and expected Akaike weights. EVOLVE simulates data along a tree using the above models. DISTTREE computes least squares branch lengths from distance matrices on a given tree, and can also construct Neighbor-Joining and UPGMA trees. REWRITE converts data sets between different formats. nucleotides and amino acid data, to estimate of maximum-likelihood branch lengths on trees (incl. clock trees and dated tips), for statistical (e.g., Shimodaira-Hasegawa) and topological (Robinson-Foulds) comparison of trees, to infer demographic parameters from trees (based on the coalescent), and also utility programs to reformat and modify alignments. There are also 6 other programs with a command-line interface which can estimate demographic parameters from coalescent trees, compute distance matrices from trees, reroot trees, and carry out some manipulations of data sets. Vanilla has a menu-based interface. It is written in Java, and is available from its web…

W2H
type: NamedIndividual
type: Sequence Management Program

weighbor
type: NamedIndividual
type: Distance Based Method

Willson quartets programs
type: NamedIndividual
type: Quartets Program

Winboot
type: NamedIndividual
type: General purpose packages program

WINCLADA
type: NamedIndividual
type: Tree Plotting Darwing Program
description: Kevin Nixon of the L. H. Bailey Hortorium at Cornell University in Ithaca, New York (kcn2 (at) cornell.edu) has written WINCLADA version 0.9.99m24, an interactive program that can read and edit trees and data files, display character state changes inferred by parsimony on diagrams of the trees, and launch runs of the programs NONA, PIWE, and Hennig86. WINCLADA is available as a Windows95/98/NT executable from its web site at http://www.cladistics.com/about_winc.htm. It is available on a shareware basis: the user who downloads it must pay $50 to Kevin Nixon at Winclada/Kevin C. Nixon, 2210 Ellis Hollow Road, Ithaca, New York 14850. There is also a $200-per-class fee for its use in courses. WINCLADA supersedes and combines features of Nixon's earlier programs ClaDOS and DADA, which are no longer distributed.

SIFTER
type: NamedIndividual
type: Bayesian Program
comment: Download application on: http://sifter.berkeley.edu
description: The Statistical Inference of Function Through Evolutionary Relationships (SIFTER) framework uses a statistical graphical model that applies phylogenetic principles to automate precise protein function prediction. http://www.ncbi.nlm.nih.gov/pubmed/21784873
label: Statistical Inference of Function Through Evolutionary Relationships

ClustalW2
type: NamedIndividual
type: General MSA Program
description: ClustalW2 is a multiple sequence alignment tool for the alignment of DNA or protein sequences. ClustalW2 calculates the best match for the input sequences based on the parameters entered and generates an easy to interpret report. This sequence alignment report displays the optimal alignment score, the alignment between sequences in a form such that the identities,similarities and differences can be clearly seen and a guide tree of the evolutionary relationships of aligned sequences.

Clustal_Omega
type: NamedIndividual
type: General MSA Program

Clustal
type: NamedIndividual
type: General MSA Program

ClustalV
type: NamedIndividual
type: General MSA Program

ClustalX
type: NamedIndividual
type: General MSA Program

EMBOSS prettyplot
type: NamedIndividual
type: Tree Plotting Darwing Program
comment: Draw a sequence alignment with pretty formatting: http://emboss.open-bio.org/rel/dev/apps/prettyplot.html
description: prettyplot draws. http://emboss.open-bio.org/wiki/Appdocs a plot of the input sequence alignment. The sequences are rendered in pretty formatting on the specified graphics device. Drawing options control the appearance of the image, such as boxes, colour and shading for highlighting conserved regions.
label: Prettyplot

EMMA
type: NamedIndividual
type: General MSA Program
comment: Multiple sequence alignment (ClustalW wrapper)
description: EMMA calculates the multiple alignment of nucleic acid or protein sequences according to the method of Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994).

PhyloH
type: NamedIndividual
type: Information Theory Based Program
comment: https://github.com/svicario/phyloH
description: Partitioning the total entropy of a data set, named ?, in intra-groups, called ?, and inter-groups, called ? components. The entropy use is the phylogenetic entropy sensu Chao et al.(2010) that take in account how the object observed are not all equally different from each other but they have a dissimilarity structure described the user supplied p hylogeny.

GeoKS
type: NamedIndividual
type: Bayesian Program
description: Estimate the probability of convergence for a phylogenetic inference performed with MrBayes by comparing the degree of overlap among different independent run of MrBayes on the same data and model.

CLIQUE
type: NamedIndividual
type: Branch And Bound Tree Search Program

CONSENSE
type: NamedIndividual
type: Tree Plotting Darwing Program
description: Computes consensus trees by the majority-rule consensus tree method, which also allows one to easily find the strict consensus tree. Is not able to compute the Adams consensus tree. Trees are input in a tree file in standard nested-parenthesis notation, which is produced by many of the tree estimation programs in the package. This program can be used as the final step in doing bootstrap analyses for many of the methods in the package.

CONTML
type: NamedIndividual
type: Heuristic Search For Best Tree Program
description: Estimates phylogenies from gene frequency data by maximum likelihood under a model in which all divergence is due to genetic drift in the absence of new mutations. Does not assume a molecular clock. An alternative method of analyzing this data is to compute Nei's genetic distance and use one of the distance matrix programs.

CONTRAST
type: NamedIndividual
type: Branch And Bound Tree Search Program
description: Reads a tree from a tree file, and a data set with continuous characters data, and produces the independent contrasts for those characters, for use in any multivariate statistics package. Will also produce covariances, regressions and correlations between characters for those contrasts. Can also correct for within-species sampling variation when individual phenotypes are available within a population.

DNACOMP
type: NamedIndividual
type: Heuristic Search For Best Tree Program
description: Estimates phylogenies from nucleic acid sequence data using the compatibility criterion, which searches for the largest number of sites which could have all states (nucleotides) uniquely evolved on the same tree. Compatibility is particularly appropriate when sites vary greatly in their rates of evolution, but we do not know in advance which are the less reliable ones.

DNADIST
type: NamedIndividual
type: Sequence Management Program
description: Computes four different distances between species from nucleic acid sequences. The distances can then be used in the distance matrix programs. (See the Distance Matrix programs pages for information on them). The distances are the Jukes-Cantor formula, one based on Kimura's 2- parameter method, the F84 model used in DNAML, and the LogDet distance. The distances can also be corrected for gamma-distributed and gamma-plus-invariant-sites-distributed rates of change in different sites. Rates of evolution can vary among sites either in a prespecified way, or according to a Hidden Markov model. The program can also make a table of percentage similarity among sequences.

DNAINVAR
type: NamedIndividual
type: Other Disances-based Program
comment: http://evolution.genetics.washington.edu/phylip/doc/dnainvar.html
description: For nucleic acid sequence data on four species, computes Lake's and Cavender's phylogenetic invariants, which test alternative tree topologies. The program also tabulates the frequencies of occurrence of the different nucleotide patterns. Lake's invariants are the method which he calls "evolutionary parsimony".

DNAM
type: NamedIndividual
type: Heuristic Search For Best Tree Program
description: Estimates phylogenies from nucleotide sequences by maximum likelihood. The model employed allows for unequal expected frequencies of the four nucleotides, for unequal rates of transitions and transversions, and for different (prespecified) rates of change in different categories of sites, and also use of a Hidden Markov model of rates, with the program inferring which sites have which rates. This also allows gamma-distribution and gamma-plus-invariant sites distributions of rates across sites.

DNAMLK
type: NamedIndividual
type: Heuristic Search For Best Tree Program
description: Same as DNAML but assumes a molecular clock. The use of the two programs together permits a likelihood ratio test of the molecular clock hypothesis to be made.

DNAMOVE
type: NamedIndividual
type: Tree Plotting Darwing Program
description: Interactive construction of phylogenies from nucleic acid sequences, with their evaluation by parsimony and compatibility and the display of reconstructed ancestral bases. This can be used to find parsimony or compatibility estimates by hand.

DNAPARS
type: NamedIndividual
type: Heuristic Search For Best Tree Program
has phylogenetic method: ML
has phylogenetic method: Likelihood
description: Estimates phylogenies by the parsimony method using nucleic acid sequences. Allows use the full IUB ambiguity codes, and estimates ancestral nucleotide states. Gaps treated as a fifth nucleotide state. It can also fo transversion parsimony. Can cope with multifurcations, reconstruct ancestral states, use 0/1 character weights, and infer branch lengths.

DNAPENNY
type: NamedIndividual
type: Branch And Bound Tree Search Program
description: Finds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search. This may not be practical (depending on the data) for more than 10 or 11 species.

DOLLOP
type: NamedIndividual
type: Heuristic Search For Best Tree Program

DOLMOVE
type: NamedIndividual
type: Tree Plotting Darwing Program

DOLPENNY
type: NamedIndividual
type: Branch And Bound Tree Search Program

DRAWGRAM
type: NamedIndividual
type: Tree Plotting Darwing Program
description: Plots rooted phylogenies, cladograms, circular trees and phenograms in a wide variety of user-controllable formats. The program is interactive and allows previewing of the tree on PC, Macintosh, or X Windows screens, or on Tektronix or Digital graphics terminals. Final output can be to a file formatted for one of the drawing programs, for a ray-tracing or VRML browser, or one at can be sent to a laser printer (such as Postscript or PCL-compatible printers), on graphics screens or terminals, on pen plotters or on dot matrix printers capable of graphics. Select here to see a sample plot.

DRAWTREE
type: NamedIndividual
type: Tree Plotting Darwing Program
description: Similar to DRAWGRAM but plots unrooted phylogenies. Select here to see a sample plot.

FACTOR
type: NamedIndividual
type: Sequence Management Program

FITCH
type: NamedIndividual
type: Heuristic Search For Best Tree Program
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ
description: Estimates phylogenies from distance matrix data under the "additive tree model" according to which the distances are expected to equal the sums of branch lengths between the species. Uses the Fitch-Margoliash criterion and some related least squares criteria, or the Minimum Evolution distance matrix method. Does not assume an evolutionary clock. This program will be useful with distances computed from molecular sequences, restriction sites or fragments distances, with DNA hybridization measurements, and with genetic distances computed from gene frequencies.

GENDIST
type: NamedIndividual
type: Sequence Management Program
description: Computes one of three different genetic distance formulas from gene frequency data. The formulas are Nei's genetic distance, the Cavalli-Sforza chord measure, and the genetic distance of Reynolds et. al. The former is appropriate for data in which new mutations occur in an infinite isoalleles neutral mutation model, the latter two for a model without mutation and with pure genetic drift. The distances are written to a file in a format appropriate for input to the distance matrix programs.

KITSCH
type: NamedIndividual
type: Heuristic Search For Best Tree Program
description: Estimates phylogenies from distance matrix data under the "ultrametric" model which is the same as the additive tree model except that an evolutionary clock is assumed. The Fitch-Margoliash criterion and other least squares criteria, or the Minimum Evolution criterion are possible. This program will be useful with distances computed from molecular sequences, restriction sites or fragments distances, with distances from DNA hybridization measurements, and with genetic distances computed from gene frequencies.

MIX
type: NamedIndividual
type: Heuristic Search For Best Tree Program

MOVE
type: NamedIndividual
type: Tree Plotting Darwing Program

NEIGHBOR
type: NamedIndividual
type: Heuristic Search For Best Tree Program
has phylogenetic method: ML
has phylogenetic method: Likelihood
has phylogenetic method: NJ
has phylogenetic method: UPGMA
description: An implementation by Mary Kuhner and John Yamato of Saitou and Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage clustering) method. Neighbor Joining is a distance matrix method producing an unrooted tree without the assumption of a clock. UPGMA does assume a clock. The branch lengths are not optimized by the least squares criterion but the methods are very fast and thus can handle much larger data sets.

PARS
type: NamedIndividual
type: Heuristic Search For Best Tree Program
has phylogenetic method: Likelihood

PENNY
type: NamedIndividual
type: Branch And Bound Tree Search Program

PROML
type: NamedIndividual
type: Heuristic Search For Best Tree Program
has phylogenetic method: ML
description: Estimates phylogenies from protein amino acid sequences by maximum likelihood. The PAM, JTT, or PMB models can be employed, and also use of a Hidden Markov model of rates, with the program inferring which sites have which rates. This also allows gamma-distribution and gamma-plus-invariant sites distributions of rates across sites. It also allows different rates of change at known sites.

PROMLK
type: NamedIndividual
type: Heuristic Search For Best Tree Program
description: Same as PROML but assumes a molecular clock. The use of the two programs together permits a likelihood ratio test of the molecular clock hypothesis to be made.

PROTDIST
type: NamedIndividual
type: Sequence Management Program
description: Computes a distance measure for protein sequences, using maximum likelihood estimates based on the Dayhoff PAM matrix, the JTT matrix model, the PBM model, Kimura's 1983 approximation to these, or a model based on the genetic code plus a constraint on changing to a different category of amino acid. The distances can also be corrected for gamma-distributed and gamma-plus-invariant-sites-distributed rates of change in different sites. Rates of evolution can vary among sites in a prespecified way, and also according to a Hidden Markov model. The program can also make a table of percentage similarity among sequences. The distances can then be used in the distance matrix programs.

PROTPARS
type: NamedIndividual
type: Heuristic Search For Best Tree Program
has phylogenetic method: ML
has phylogenetic method: Likelihood
description: Estimates phylogenies from protein sequences (input using the standard one-letter code for amino acids) using the parsimony method, in a variant which counts only those nucleotide changes that change the amino acid, on the assumption that silent changes are more easily accomplished.

RESTDIST
type: NamedIndividual
type: Sequence Management Program
description: Distances calculated from restriction sites data or restriction fragments data. The restriction sites option is the one to use to also make distances for RAPDs or AFLPs.

RESTML
type: NamedIndividual
type: Heuristic Search For Best Tree Program
description: Estimation of phylogenies by maximum likelihood using restriction sites data (not restriction fragments but presence/absence of individual sites). It employs the Jukes-Cantor symmetrical model of nucleotide change, which does not allow for differences of rate between transitions and transversions. This program is VERY slow.

RETREE
type: NamedIndividual
type: Tree Plotting Darwing Program
description: Reads in a tree (with branch lengths if necessary) and allows you to reroot the tree, to flip branches, to change species names and branch lengths, and then write the result out. Can be used to convert between rooted and unrooted trees, and to write the tree into a preliminary version of a new XML tree file format which is under development and which is described in the RETREE documentation web page.

SEQBOOT
type: NamedIndividual
type: Sequence Management Program
description: Reads in a data set, and produces multiple data sets from it by bootstrap resampling. Since most programs in the current version of the package allow processing of multiple data sets, this can be used together with the consensus tree program CONSENSE to do bootstrap (or delete-half-jackknife) analyses with most of the methods in this package. This program also allows the Archie/Faith technique of permutation of species within characters. It can also rewrite a data set to convert it from between the PHYLIP Interleaved and Sequential forms, and into a preliminary version of a new XML sequence alignment format which is under development and which is described in the SEQBOOT documentation web page.

TREEDIST
type: NamedIndividual
type: Tree Plotting Darwing Program
description: Computes the Branch Score distance between trees, which allows for differences in tree topology and which also makes use of branch lengths. Also computes the Robinson-Foulds symmetric difference distance between trees, which allows for differences in tree topology but does not use branch lengths.

Distance Wangner
type: NamedIndividual
type: Distance Based Method
description: The distance-Wagner method is intended as an approximation to construction of a most parsimonious tree. Species are added to a tree, each in the best possible place. This is judged by computation of the increase in the length of the tree caused by each possible placement of that species.

TREEDIST
type: NamedIndividual
type: Tree Plotting Darwing Program
description: Computes the Branch Score distance between trees, which allows for differences in tree topology and which also makes use of branch lengths. Also computes the Robinson-Foulds symmetric difference distance between trees, which allows for differences in tree topology but does not use branch lengths.

UPGMA
type: NamedIndividual
type: Distance Based Method
description: Unweighted Pair Group Method with Arithmetic Mean This method applies a particular algorithm to a distance matrix to come up with a tree directly.At each step, the nearest two clusters are combined into a higher-level cluster. The distance between any two clusters A and B is taken to be the average of all distances between pairs of objects "x" in A and "y" in B, that is, the mean distance between elements of each cluster.

Nearest Neighbor Interchange
type: NamedIndividual
type: Branch And Bound Tree Search Program
description: Nearest Neighbor Interchange is a heuristic algorithm for searching through treespace. It proceeds by juxtaposing the positions of neighbors on a phylogenetic tree. If the resulting tree is better, then it is retained.
label: Nni

SPR
type: NamedIndividual
type: Branch And Bound Tree Search Program
description: Subtree Pruning Regrafting is a heuristic search algorithm for searching through treespace. It proceeds by breaking off part of the tree and attaching it to another part of the tree. If it finds a better tree, then the new tree is used as a starting tree for another round of SPR. This is a more rigorous algorithm than NNI. Another name for SPR is cut-and-paste.
label: Subtree Pruning Regrafting

BLASTSIMPLIFIER
type: NamedIndividual
type: Sequence Management Program
comment: WSDL Location: http://phoebus.cs.man.ac.uk:1977/axis/services/seq_analysis.blastsimplifier?wsdl
description: Simplifies BLAST output for later use

iTOL
type: NamedIndividual
type: Tree Plotting Darwing Program

nuclear sequence
type: NamedIndividual
type: Sequence
has aligned by: DECIPHER
has aligned by: Geneious
has aligned by: Kalign
has aligned by: MAFFT
has aligned by: MSA
has aligned by: MUSCLE
has aligned by: Opal
has aligned by: Phylo
has aligned by: Praline
has aligned by: POA
has aligned by: Probalign
has aligned by: ProbCons
has aligned by: PROMALS3D
has aligned by: SAGA
has aligned by: SAM
has aligned by: Se-Al
has aligned by: T-Coffee
has aligned by: ClustalW
has aligned by: CodonCode Aligner
has aligned by: ALIGN
has aligned by: ARB
has aligned by: Bio++
has aligned by: DAMBE
has aligned by: EMBOSS
has aligned by: GeneDoc
has aligned by: MacClade
has aligned by: MEGA
has aligned by: Mesquite
has aligned by: MrModeltest
has aligned by: PAUP
has aligned by: PHYLIP
has aligned by: PHYML
has aligned by: ProtTest
has aligned by: RAxML
has aligned by: SeaView
has aligned by: SeqPup
has aligned by: ClustalW2
has aligned by: Clustal
has aligned by: ClustalV
has collected by: PSI-BLAST
has collected by: BLASTX
has collected by: TBLASTX
has collected by: megaBLAST
has collected by: TBLASTN
has collected by: matcher
has collected by: SIM
has collected by: water
has collected by: NAP
has collected by: BLAST
has collected by: BLASTP
has collected by: BLASTN
has collected by: BioEdit
has collected by: PHYDIT
has collected by: PHYLIP
has collected by: DNADIST
has collected by: PROTDIST
has collected by: SEQBOOT
has hypothesis validated by: ARB
has hypothesis validated by: BEAST
has hypothesis validated by: Bionumerics
has hypothesis validated by: DAMBE
has hypothesis validated by: ELW
has hypothesis validated by: Geneious
has hypothesis validated by: MEGA
has hypothesis validated by: ModelTest
has hypothesis validated by: Modeltest
has hypothesis validated by: MrModeltest
has hypothesis validated by: Network
has hypothesis validated by: PAUP
has hypothesis validated by: PHYLIP
has hypothesis validated by: PHYML
has hypothesis validated by: ProtTest
has hypothesis validated by: RAxML
has hypothesis validated by: raxmlGUI
has hypothesis validated by: SeaView
has hypothesis validated by: TREECON