Phyml

Modified to analyze coding sequences

Phyml original version

Authors: Guidon s. and Gascual O.
Reference: Systematic Biology 52(5):696-704
Document: /usr/local/phylogeny/phyml/doc/phyml_manual.pdf

Phyml modified for the analysis of coding sequences

Author: Miyazwa S.
Help File: not available yet.

Alignment


Alignment type :

Code table :

Initial tree in newick format

Method

Equilibrium frequencies:
Variation over sites
Model for selective Constraints on amino acids:
ML parameters:

ML parameters settings explanation
1: (w0; non-/synonymous rate ratio only)
5: (β, w0, σ, m, mtc|ag / m[tc][ag], mag / mtc[ag])
8: (β, w0, σ, m, mtc|ag / m[tc][ag], mag / mtc[ag], fa, fc, fg)
12: (β, w0, σ, m, mtc|ag / m[tc][ag], mag / mtc[ag], mta / m[tc][ag], mtg / m [tc][ag], mca / m[tc][ag], fa, fc, fg)

Initial values for parameters: Estimates for
or
Additional options:

Optimize tree

(Note: The optimization should be done only if a simple substitution model is used.)