xenial (1) phyml.1.gz

Provided by: phyml_3.2.0+dfsg-1_amd64 bug

NAME

       phyml - 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
              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.

       -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, 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.

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 <tille@debian.org>, for the Debian project (but may be used
       by others).