Phyml

modified to analyze coding sequences

Phyml original version

Authors: Guidon, S. and Gascual, O.
Reference: Systematic Biology 52(5):696-704
Document: http://code.google.com/p/phyml

Modified to analyze coding sequences

Author: Miyazawa, S.
Document: not available yet.

Alignment


Alignment type :

Code table :

First base for each codon: TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Second base for each codon: TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Third base for each codon: TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Symbol for each codon: ?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
Universal codon table: FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Mitochondrial codon table: FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG

Initial tree in newick format

Method

Amino Acid substitution model
Equilibrium frequencies:
Model:
Custom(6 digits string):
Variation over sites
Discrete Gamma:
Initial values for alpha(shape parameter):
Optimize α:
Codon substitution model
Equilibrium frequencies:
Variation over sites
Discrete Gamma:
Initial values for alpha(shape parameter):
Optimize α:
Model for selective Constraints on amino acids:
ML parameters:

ML parameters settings explanation
0: All parameters are fixed at the initial value.
1: (w0; non-/synonymous rate ratio only)
4: (β, w0, σ = 0, m, mtc|ag / m[tc][ag], mag / mtc|ag)
5: (β, w0, σ, m, mtc|ag / m[tc][ag], mag / mtc|ag)
7: (β, w0, σ = 0, m, mtc|ag / m[tc][ag], mag / mtc|ag, fa, fc, fg)
8: (β, w0, σ, m, mtc|ag / m[tc][ag], mag / mtc|ag, fa, fc, fg)
11: (β, w0, σ = 0, m, mtc|ag / m[tc][ag], mag / mtc|ag, mta / m[tc][ag], mtg / m [tc][ag], mca / m[tc][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
Probability of neutral substitutions between amino acids a and b: approximated by exp(βwab + w0(1-δab))
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 [mij]:
ratio (m) of double/triple to single/double nucleotide changes: Default
mtc|ag / m[tc][ag] (transition to transversion rate ratio): Default
mag / mtc|ag: Default
mta / m[tc][ag]: Default
mtg / m[tc][ag]: Default
mca / m[tc][ag]: Default
Initial values of nucleotide equilibrium frequencies [fi]:
fa: Default
fc: Default
fg: Default
Additional options:

Optimize tree

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

See results later

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