Phyml
modified to analyze coding sequences

Help Here


----Credits----
Phyml original version
Authors: Guidon, S. and Gascual, O.
Reference: Systematic Biology 52(5):696-704
Program source: http://code.google.com/p/phyml
Phyml's version modified to analyze coding sequences
Author: Miyazawa, S.
References: PLoS One, 8, e54252/pp. 1-20, 2013
PLoS One, 6, e28892/pp. 1-20, 2011
PLoS One, 6, e17244/pp. 1-22, 2011
Patch file: http://www.sanzo.org/
This web interface
Author: Julio Claudio Matus Ramirez
Modified by: Sanzo Miyazawa

Alignment in the phylip format


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 the 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
The value 11 is recommended unless the total size of tree is small, otherwise 4.

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])
5: (β, w0, σ, m, mtc|ag / m[tc][ag])
7: (β, w0, σ = 0, m, mtc|ag / m[tc][ag], fmuta, fmutc, fmutg)
8: (β, w0, σ, m, mtc|ag / m[tc][ag], fmuta, fmutc, fmutg)
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], fmuta, fmutc, fmutg)
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], fmuta, fmutc, fmutg)
Initial values for parameters:

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 variation over time/sites): Default
Initial values of nucleotide exchangeabilities [mij]:
ratio (m) of double/triple to single/double nucleotide changes (m=0 means no opimization): 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:
Optional parameters explanation
Options: see the source program, cl.c. The followings are typical ones.

--mechanistic_opt (0|1)(0|1)(0|1)(0|1|2|5|6)(0|3)
    The number of parameters optimized in the order of beta, w_0, sigma, m, exchangeabilities, mutation equilibrium base frequencies
--mechanistic_params "-9.0 -1.5 0.0 0.0001 1.0 -9.0 -9.0 -9.0 -9.0 0.25 0.25 0.25"
    beta, w_0, sigma, 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^mut_a, f^mut_c, f^mut_g
    Selective constraint w = beta*w_est+w_0, Scale of the Gamma distribution for rate variation over time/sites, Multiple base change rate m, Exchangeabilities, Mutation equilibrium base frequencies,
    The value 0.0 for m means no optimization for m. The value -9.0 means the value estimated for the specified mutaion matrix such as JTT and LG.
--alpha 10.0 -alpha e --alpha_w 0.2 --alpha_w e --gamma_unequal 1
    --alpha e: estimation of alpha in the gamma distribution for rate variation
    --alpha_w e: estimation of alpha_w in the gamma distribution for selectiive constraint variation
    --gamma_unequal 1: discrete gamma distribution with unequal probability
-o (n|l|r|t|lr|lrt)
    n: no optimization, l: branch, r: rate, t: tree optimization

Optimize tree

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

See results later

Optionally you can have an e-mail sent to you when done.
Email address: