]>
F81
F81+1
F81+1+P
F81+P
GTR
PMID 1342937
04/04/11
Generalised time reversible. GTR is the most general neutral, independent, finite-sites, time-reversible model possible. It was first described in a general form by Simon Tavaré in 1986.[7]
The GTR parameters for nucleotides consist of an equilibrium base frequency vector, , giving the frequency at which each base occurs at each site, and the rate matrix.
ver1
Maryam Panahiazar-Dr. Leebens-Mack lab-UGA
the nucleotide GTR requires 6 substitution rate parameters and 4 equilibrium base frequency parameters.
GTR+1
GTR+1+P
GTR+P
HKY
HKY+1+P
HKY+P
HYY+1
SYM
SYM+1
SYM+1+P
SYM+P
alignment
amino acid model
ape
arlequin
bayesian inference
beast
boot strap
branch swapping
Branch Swapping as a heuristic search method. Heuristic methods are exploratory approaches that attempt an approximate solution to a particular computational problem that may be difficult or impossible to solve exactly.
http://www.mun.ca/biology/scarr/Tree_Pruning_methods.html
codon based model
consel
continuous characters
dambe
data
data format
discrete characters
distance based
fast tree
garli
hy phy
jacknife
jc
jc+1
jc+1+p
jc+P
k80
k80+1
k80+1+p
k80+p
kimura's two parameter model
logdet distances
maximum likelihood
maximum parsimony
mega
method
model
models of dna evolution
models of protein evolution
models with nonindependence of sites
molphy
mrbayes
neighbor joining
ninja
nni
Nearest-Neighbor Interchange (NNI)
http://www.mun.ca/biology/scarr/Tree_Pruning_methods.html
nona
optomality
other distances
paml
parameter
paup*
phylip
phylogenetic
poy
program
protein structure and correlated change
rate_variation_between_loci
rate_variation_between_sites
raxml
resampling
search ...
splits tree
spr
http://www.mun.ca/biology/scarr/Tree_Pruning_methods.html
Subtree Pruning & Regrafting (SPR) takes a "provisional tree" of suspected minimum length, "prunes" one branch and experimentally adds it to each of the internodes in the remaining tree.
tbr
Tree Bisection and Reconnection (TBR), in which the tree is cut as nearly in half as possible and re-grafted.
http://www.mun.ca/biology/scarr/Tree_Pruning_methods.html
the general time reversible model
the_tamura_nei_model_f84
the_tamura_nei_model_hky
tree puzzle