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 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!)
- -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.
- 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.
- 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.
- 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.
- 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).
- 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.
- 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.
- 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.
- 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.
- 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, Sytematic 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.
- 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
AUTHOR
PhyML was written by Stephane Guindon and Olivier Gascuel and othersThis manual page was written by Andreas Tille <[email protected]>, for the Debian project (but may be used by others).