WAVES '0.1.0Beta' version, mind this is beta!

PhyML - v1.0

Online since 15 Jul 2016, 2:49 p.m. / last update 6 Sep 2016, 11:18 a.m.


The nucleotide or amino-acid sequence file in PHYLIP format

An integer corresponding to the number of data sets to analyse

int > 0: int is the number of bootstrap replicates.
int = 0: neither approximate likelihood ratio test nor bootstrap values are computed.
int = -1: approximate likelihood ratio test returning aLRT statistics.
int = -2: approximate likelihood ratio test returning Chi2-based parametric branch supports.
int = -4: (default) SH-like branch supports alone.
int = -5: approximate Bayes branch supports.

model : substitution model name. - Nucleotide-based models : HKY85 (default) | JC69 | K80 | F81 | F84 | TN93 | GTR - Amino-acid based models : LG (default) | WAG | JTT | MtREV | Dayhoff | DCMut | RtREV | CpREV | VT | Blosum62 | MtMam | MtArt | HIVw | HIVb | custom

e : the character frequencies are determined as follows : - Nucleotide sequences: (Empirical) the equilibrium base frequencies are estimated by counting the occurence of the different bases in the alignment. - Amino-acid sequences: (Empirical) the equilibrium amino-acid frequencies are estimated by counting the occurence of the different amino-acids in the alignment. m : the character frequencies are determined as follows : - Nucleotide sequences: (ML) the equilibrium base frequencies are estimated using maximum likelihood - Amino-acid sequences: (Model) the equilibrium amino-acid frequencies are estimated using the frequencies defined by the substitution model. "fA,fC,fG,fT" : only valid for nucleotide-based models. fA, fC, fG and fT are floating numbers that correspond to the frequencies of A, C, G and T respectively (WARNING: do not use any blank space between your values of nucleotide frequencies, only commas!)

fA, fC, fG and fT are floating numbers that correspond to the frequencies of A, C, G and T respectively (WARNING: do not use any blank space between your values of nucleotide frequencies, only commas!)

Transition/transversion ratio. DNA sequences only. Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate.

Number of relative substitution rate categories. Default : nb_subst_cat=4.

Distribution of the gamma distribution shape parameter. Can be a fixed positive value or e to get the maximum likelihood estimate.

Starting tree. The tree must be in Newick format.

This option focuses on specific parameter optimisation

The number of initial random trees to be used. It is only valid if SPR searches are to be performed.



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