Phyml

Modified to analyze coding sequences

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

Filename:

Alignment type :

Code table :

Initial tree in newick format

None From file:

Method

Amino Acid substitution model
Equilibrium frequencies:
Model:	Custom(6 digits string):
Use an amino acid substitution model:
Variation over sites
Discrete Gamma:
Initial values for alpha(shape parameter):	Default
Optimize α:
Use Codon substitution model
Codon substitution model

Equilibrium frequencies:

Variation over sites

Discrete Gamma:

Initial values for alpha(shape parameter):

Default

Optimize α:

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, m_tc|ag / m_[tc][ag], m_ag / m_tc[ag])
8: (β, w₀, σ, m, m_tc|ag / m_[tc][ag], m_ag / m_tc[ag], f_a, f_c, f_g)
12: (β, w₀, σ, m, m_tc|ag / m_[tc][ag], m_ag / m_tc[ag], m_ta / m_[tc][ag], m_tg / m _[tc][ag], m_ca / m_[tc][ag], f_a, f_c, f_g)

Initial values for parameters:

Estimates for nuclear genes cpDNA mtDNA
or simple default values as follows

Probability of neutral substitutions between amino acids a and b: approximated by exp(βw_ab + w₀(1-δ_ab))
β	Default
w₀	Default
Mutation rate variation of Gamma distribution can be assumed.
Scale parameter of the Gamma distribution (σ = 0 means no rate variation):	Default
Initial values of nucleotide exchangeabilities [m_ij]:
ratio (m) of double/triple to single/double nucleotide changes:	Default
m_tc\|ag / m_[tc][ag] (transition to transversion rate ratio):	Default
m_ag / m_tc[ag]:	Default
m_ta / m_[tc][ag]:	Default
m_tg / m_[tc][ag]:	Default
m_ca / m_[tc][ag]:	Default
Initial values of nucleotide equilibrium frequencies [f_i]:
f_a:	Default
f_c:	Default
f_g:	Default

Additional options:

Phyml

Alignment

Alignment type :

Code table :

Initial tree in newick format

Method

Optimize tree yes no

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

Phyml

Alignment

Alignment type : codon (one-letter code) amino acid nucleotide

Code table : Universal Mitochondrial

Initial tree in newick format

Method

Optimize tree yes no

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

Alignment type :

Code table :