Additional section
Method for estimating support of branches
none
bootstrap
SH-like likelihood ratio test
approximate likelihood ratio test
likelihood ratio test using chi2
Bayesian-like transformation of likelihood ratio test

Number of trials for bootstrap

Nucleic acid evolution model
Hasegawa-Kishino-Yano
Jukes-Cantor
Kimura
Felsenstein F81
Felsenstein F84
Tamura-Nei
General Time Reversible

Protein evolution model
Le and Gascuel
Whelan and Goldman
Jones-Taylor-Thornton
model for mitochondrial proteins
Dayhoff PAM
Direct Computation with Mutabilities
model for retroviral proteins
model for chloroplast proteins
Vingron resolvent method
BLOSUM62
model for mammalian mitochondrial proteins
model for arthropod mitochondrial proteins
model for HIV
model for HIV-B

Estimate transition/transversion ratio?
Yes
No

Transition/transversion ratio

Use empirical base/amino acid frequencies?
Yes
No

Estimate proportion of invariable sites?
Yes
No

Proportion of invariable sites

Number of substitution rate categories

Estimate gamma distribution parameter?
Yes
No

Gamma distribution parameter

Starting tree
BIONJ
maximum parsimony
user provided

User provided starting tree:

Optimise tree topology?
Yes
No

Optimise branch lengths?
Yes
No

Tree topology search method
Nearest Neighbour Interchange
Subtree Pruning and Regrafting
NNI + SPR

Restart tree topology search with randomized trees?
Yes
No

Number of random restarts