Provided by: phyml_20120412-2_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).