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_nameseq_file_name is the name of the nucleotide or amino-acid sequence file in PHYLIP format.
-d (or --datatype) data_typedata_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_setsnb_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) intint>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 |
VTBlosum62 | MtMam | MtArt | HIVw | HIVb | custom--aa_rate_filefilenamefilename 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.
-fe, m, or fA,fC,fG,fTe : 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_ratiots/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_invarprop_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_catnb_subst_cat : number of relative substitution rate categories. Default: nb_subst_cat=4. Must be
a positive integer.
-a (or --alpha) gammagamma : 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_fileuser_tree_file : starting tree filename. The tree must be in Newick format.
-oparams
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_startsnumnum is the number of initial random trees to be used. It is only valid if SPR searches are to be
performed.
--r_seednumnum 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_idID_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_displaynum (default=20)
num is the frequency at which the bootstrap progress bar will be updated. Must be an integer.
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