--- name: "phyml" section: "1" platform: "linux" package: "phyml" version: "3:3.3.20220408-4+b1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/phyml" --- # phyml(1) Phylogenetic estimation using Maximum Likelihood ## NAME phyml, phyml-mpi - Phylogenetic estimation using Maximum Likelihood ## SYNOPSIS: phyml \[command args\] - All the options below are optional (except '-i' if you want to use the command-line interface). Command options: **-i** (or **--input**) *seq\_file\_name* - *seq\_file\_name* is the name of the nucleotide or amino-acid sequence file in PHYLIP format. **-d** (or **--datatype**) *data\_type* - *data\_type* is 'nt' for nucleotide (default), 'aa' for amino-acid sequences, or 'generic', (use NEXUS file format and the 'symbols' parameter here). **-q** (or **--sequential**) - Changes interleaved format (default) to sequential format. **-n** (or **--multiple**) *nb\_data\_sets* - *nb\_data\_sets* is an integer corresponding to the number of data sets to analyse. **-p** (or **--pars**) Use a minimum parsimony starting tree. This option is taken into account when the '-u' option is absent and when tree topoLOGy modifications are to be done. **-b** (or **--bootstrap**) *int* - *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. **-m** (or **--model**) *model* - model : substitution model name. - *Nucleotide*-based models : *HKY85* (default) \| *JC69* \| *K80* \| *F81* \| *F84* \| *TN93* \| *GTR* \| *custom* (for the custom option, a string of six digits identifies the model. For instance, 000000) - corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform). 012345 corresponds to GTR. This option can be used for encoding any model that is a nested within GTR. - \- *Amino-acid* based models : *LG* (default) \| *WAG* \| *JTT* \| *MtREV* \| *Dayhoff* \| *DCMut* \| *RtREV* \| *CpREV* \| *VT* *Blosum62* \| *MtMam* \| *MtArt* \| *HIVw* \| *HIVb* \| *custom* **--aa\_rate\_file** *filename* - *filename* is the name of the file that provides the amino acid substitution rate matrix in PAML format. It is compulsory to use this option when analysing amino acid sequences with the \`custom' model. **-f** *e*, *m*, or *fA,fC,fG,fT* - *e* : the character frequencies are determined as follows : - \- Nucleotide sequences: (Empirical) the equilibrium base frequencies are estimated by counting the occurrence of the different bases in the alignment. - \- Amino-acid sequences: (Empirical) the equilibrium amino-acid frequencies are estimated by counting the occurrence 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!) **-t** (or **--ts**/tv) *ts/tv\_ratio* - *ts/tv\_ratio* : transition/transversion ratio. DNA sequences only. Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate. **-v** (or **--pinv**) *prop\_invar* - *prop\_invar*: proportion of invariable sites. Can be a fixed value in the \[0,1\] range or e to get the maximum likelihood estimate. **-c** (or **--nclasses**) *nb\_subst\_cat* - *nb\_subst\_cat* : number of relative substitution rate categories. Default: *nb\_subst\_cat=4*. Must be a positive integer. **-a** (or **--alpha**) *gamma* - *gamma* : distribution of the gamma distribution shape parameter. Can be a fixed positive value or *e* to get the maximum likelihood estimate. **-s** (or **--search**) *move* - Tree topoLOGy search operation option. Can be either *NNI* (default, fast) or *SPR* (a bit slower than NNI) or *BEST* (best of NNI and SPR search). **-u** (or **--inputtree**) *user\_tree\_file* - *user\_tree\_file* : starting tree filename. The tree must be in Newick format. **-o** *params* - This option focuses on specific parameter optimisation. - *params*=tlr : tree topoLOGy (t), branch length (l) and rate parameters (r) are optimised. - *params*=tl : tree topoLOGy and branch length are optimised. - *params*=lr : branch length and rate parameters are optimised. - *params*=l : branch length are optimised. - *params*=r : rate parameters are optimised. - *params*=n : no parameter is optimised. **--rand\_start** - This option sets the initial tree to random. It is only valid if SPR searches are to be performed. **--n\_rand\_starts** *num* - *num* is the number of initial random trees to be used. It is only valid if SPR searches are to be performed. **--r\_seed** *num* - *num* is the seed used to initiate the random number generator. Must be an integer. **--print\_site\_lnl** - Print the likelihood for each site in file \*\_phyml\_lk.txt. **--print\_trace** - Print each phyLOGeny explored during the tree search process in file \*\_phyml\_trace.txt. **--run\_id** *ID\_string* - Append the string *ID\_string* at the end of each PhyML output file. This option may be useful when running simulations involving PhyML. **--quiet** - No interactive question (for running in batch mode) and quiet output. **--no\_memory\_check** - No interactive question for memory usage (for running in batch mode). Normal output otherwise. **--alias\_subpatt** - Site aliasing is generalized at the subtree level. Sometimes lead to faster calculations. See Kosakovsky Pond SL, Muse SV, Systematic Biology (2004) for an example. **--boot\_progress\_display** *num* (default=20) - *num* is the frequency at which the bootstrap progress bar will be updated. Must be an integer. ## PHYLIP-LIKE INTERFACE You can also use PhyML with no argument, in this case change the value of a parameter by typing its corresponding character as shown on screen. ## EXAMPLES DNA interleaved sequence file, default parameters : - **phyml -i seqs1** AA interleaved sequence file, default parameters : - **phyml -i seqs2 -d aa** - AA sequential sequence file, with customization : - **phyml -i seqs3 -q -d aa -m JTT -c 4 -a e** ## SEE ALSO A simple, fast, and accurate algorithm to estimate large phyLOGenies by maximum likelihood Stephane Guindon and Olivier Gascuel, Systematic BioLOGy 52(5):696-704, 2003. Please cite this paper if you use this software in your publications. ## AUTHOR **PhyML** was written by Stephane Guindon and Olivier Gascuel and others This manual page was written by Andreas Tille \, for the Debian project (but may be used by others).