NAME

Bio::Tools::Run::Phylo::Phyml - Wrapper for rapid reconstruction of phylogenies using Phyml

SYNOPSIS

  use Bio::Tools::Run::Phylo::Phyml;

  #  Make a Phyml factory
  $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => 2);
  # it defaults to protein alignment
  # change parameters
  $factory->model('Dayhoff');
  #  Pass the factory an alignment and run
  $inputfilename = 't/data/protpars.phy';
  $tree = $factory->run($inputfilename); # $tree is a Bio::Tree::Tree object.


  # or set parameters at object creation
  my %args = (
      -data_type => 'dna',
      -model => 'HKY',
      -kappa => 4,
      -invar => 'e',
      -category_number => 4,
      -alpha => 'e',
      -tree => 'BIONJ',
      -opt_topology => '0',
      -opt_lengths => '1',
      );
  $factory = Bio::Tools::Run::Phylo::Phyml->new(%args);
  # if you need the output files do
  $factory->save_tempfiles(1);
  $factory->tempdir($workdir);

  # and get a Bio::Align::AlignI (SimpleAlign) object from somewhere
  $tree = $factory->run($aln);

DESCRIPTION

This is a wrapper for running the phyml application by Stephane Guindon and Olivier Gascuel. You can download it from: http://atgc.lirmm.fr/phyml/

Installing

After downloading, you need to rename a the copy of the program that runs under your operating system. I.e. "phyml_linux" into "phyml".

You will need to help this Phyml wrapper to find the "phyml" program. This can be done in (at least) three ways:

1.

Make sure the Phyml executable is in your path. Copy it to, or create a symbolic link from a directory that is in your path.

2.

Define an environmental variable PHYMLDIR which is a directory which contains the 'phyml' application: In bash:

  export PHYMLDIR=/home/username/phyml_v2.4.4/exe

In csh/tcsh:

  setenv PHYMLDIR /home/username/phyml_v2.4.4/exe

3.

Include a definition of an environmental variable PHYMLDIR in every script that will use this Phyml wrapper module, e.g.:

  BEGIN { $ENV{PHYMLDIR} = '/home/username/phyml_v2.4.4/exe' }
  use Bio::Tools::Run::Phylo::Phyml;

This wrapper has been tested with PHYML v2.4.4 and v.3.0. It may work with recent Phyml releases using a date format for the format, but the wrapper hasn't been extensively tested in these cases, so for the moment only the simpler numbered versions are supported.

In its current state, the wrapper supports only input of one MSA and output of one tree. It can easily be extended to support more advanced capabilities of "phyml".

Two convienience methods have been added on top of the standard BioPerl WrapperBase ones: stats() and tree_string(). You can call them to after running the phyml program to retrieve into a string the statistics and the tree in Newick format.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

AUTHOR - Heikki Lehvaslaiho

heikki at bioperl dot org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : $factory = Bio::Tools::Run::Phylo::Phyml->new(@params)
 Function: creates a new Phyml factory
 Returns : Bio::Tools::Run::Phylo::Phyml
 Args    : Optionally, provide any of the following (default in []):
           -data_type       => 'dna' or 'protein',   [protein]
           -dataset_count   => integer,             [1]
           -model           => 'HKY'... ,            [HKY|JTT]
           -kappa           => 'e' or float,         [e]
           -invar           => 'e' or float,         [e]
           -category_number => integer,              [1]
           -alpha           => 'e' or float (int v3),[e]
           -tree            => 'BIONJ' or your own,  [BION]
           -bootstrap       => integer               [123]
           -opt_topology    => boolean               [1]
           -opt_lengths     => boolean               [1]
           -no_memory_check => boolean               [1]
           -program_name    => string

program_name

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns : string
 Args    : None

program_dir

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns : string
 Args    : None

version

 Title   : version
 Usage   : exit if $prog->version < 1.8
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none

Phyml before 3.0 did not display the version. Assume 2.44 when can not determine it.

Some releases do not state version number, only date, so the version might have to be inferred from this date.

run

 Title   : run
 Usage   : $factory->run($aln_file);
           $factory->run($align_object);
 Function: Runs Phyml to generate a tree
 Returns : Bio::Tree::Tree object
 Args    : file name for your input alignment in a format
           recognised by AlignIO, OR  Bio::Align::AlignI
           compliant object (eg. Bio::SimpleAlign).

stats

 Title   : stats
 Usage   : $factory->stats;
 Function: Returns the contents of the phyml '_phyml_stat.txt' output file
 Returns : string with statistics about the run, undef before run()
 Args    : none

tree_string

 Title   : tree_string
 Usage   : $factory->tree_string;
           $factory->run($align_object);
 Function: Returns the contents of the phyml '_phyml_tree.txt' output file
 Returns : string with tree in Newick format, undef before run()
 Args    : none

Getsetters

These methods are used to set and get program parameters before running.

data_type

 Title   : data_type
 Usage   : $phyml->data_type('nt');
 Function: Sets sequence alphabet to 'dna' (nt in v3) or 'aa'
           If leaved unset, will be set automatically
 Returns : set value, defaults to  'protein'
 Args    : None to get, 'dna' ('nt') or 'aa' to set.

data_format

 Title   : data_format
 Usage   : $phyml->data_format('s');
 Function: Sets PHYLIP format to 'i' interleaved or
           's' sequential
 Returns : set value, defaults to  'i'
 Args    : None to get, 'i' or 's' to set.

dataset_count

 Title   : dataset_count
 Usage   : $phyml->dataset_count(3);
 Function: Sets dataset number to deal with
 Returns : set value, defaults to 1
 Args    : None to get, positive integer to set.

model

 Title   : model
 Usage   : $phyml->model('HKY');
 Function: Choose the substitution model to use. One of

           JC69 | K2P | F81 | HKY | F84 | TN93 | GTR (DNA)
           JTT | MtREV | Dayhoff | WAG (amino acids)

           v3.0:
           HKY85 (default) | JC69 | K80 | F81 | F84 |
           TN93 | GTR (DNA)
           LG (default) | WAG | JTT | MtREV | Dayhoff | DCMut |
           RtREV | CpREV | VT | Blosum62 | MtMam | MtArt |
           HIVw |  HIVb (amino acids)

 Returns : Name of the model, v2.4.4 defaults to {HKY|JTT}
 Args    : None to get, string to set.

kappa

 Title   : kappa
 Usage   : $phyml->kappa(4);
 Function: Sets transition/transversion ratio, leave unset to estimate
 Returns : set value, defaults to 'e'
 Args    : None to get, float or integer to set.

invar

 Title   : invar
 Usage   : $phyml->invar(.3);
 Function: Sets proportion of invariable sites, leave unset to estimate
 Returns : set value, defaults to 'e'
 Args    : None to get, float or integer to set.

category_number

 Title   : category_number
 Usage   : $phyml->category_number(4);
 Function: Sets number of relative substitution rate categories
 Returns : set value, defaults to 1
 Args    : None to get, integer to set.

alpha

 Title   : alpha
 Usage   : $phyml->alpha(1.0);
 Function: Sets  gamma distribution parameter, leave unset to estimate
 Returns : set value, defaults to 'e'
 Args    : None to get, float or integer to set.

tree

 Title   : tree
 Usage   : $phyml->tree('/tmp/tree.nwk');
 Function: Sets starting tree, leave unset to estimate a distance tree
 Returns : set value, defaults to 'BIONJ'
 Args    : None to get, newick tree file name to set.

v2 options

These methods can be used with PhyML v2* only.

opt_topology

 Title   : opt_topology
 Usage   : $factory->opt_topology(1);
 Function: Choose to optimise the tree topology
 Returns : 1 or 0. Default is 1.
 Args    : None to get, boolean to set.

v2.* only

opt_lengths

 Title   : opt_lengths
 Usage   : $factory->opt_lengths(0);
 Function: Choose to  optimise branch lengths and rate parameters
 Returns : 1 or 0. Default is 1.
 Args    : None to get, boolean to set.

v2.* only

v3 options

These methods can be used with PhyML v3* only.

freq

 Title   : freq
 Usage   : $phyml->freq(e); $phyml->freq("0.2, 0.6, 0.6, 0.2");
 Function: Sets nucleotide frequences or asks residue to be estimated
            according to two models: e or d
 Returns : set value,
 Args    : None to get, string to set.

v3 only.

opt

 Title   : opt
 Usage   : $factory->opt(1);
 Function: Optimise tree parameters: tlr|tl|tr|l|n
 Returns : {value|n} (default n)
 Args    : None to get, string to set.

v3.* only

search

 Title   : search
 Usage   : $factory->search(SPR);
 Function: Tree topology search operation algorithm: NNI|SPR|BEST
 Returns : string (defaults to NNI)
 Args    : None to get, string to set.

v3.* only

rand_start

 Title   : rand_start
 Usage   : $factory->rand_start(1);
 Function: Sets the initial SPR tree to random.
 Returns : boolean (defaults to false)
 Args    : None to get, boolean to set.

v3.* only; only meaningful if $prog->search is 'SPR'

rand_starts

 Title   : rand_starts
 Usage   : $factory->rand_starts(10);
 Function: Sets the number of initial random SPR trees
 Returns : integer (defaults to 1)
 Args    : None to get, integer to set.

v3.* only; only valid if $prog->search is 'SPR'

rand_seed

 Title   : rand_seed
 Usage   : $factory->rand_seed(1769876);
 Function: Seeds the random number generator
 Returns : random integer
 Args    : None to get, integer to set.

v3.* only; only valid if $prog->search is 'SPR'

Uses perl rand() to initialize if not explicitely set.

no_memory_check

 Title   : no_memory_check
 Usage   : $factory->no_memory_check(1);
 Function:
 Returns : boolean (defaults to false)
 Args    : None to get, integer to set.

bootstrap

 Title   : bootstrap
 Usage   : $factory->bootstrap(100);
 Function: Set number of bootstraps
 Returns :
 Args    : None to get, integer to set.

command

 Title   : command
 Usage   : $factory->command(...);
 Function:
 Returns : string
 Args    : None to get, integer to set.

Internal methods

These methods are private and should not be called outside this class.

_setparams

 Title   : _setparams
 Usage   : Internal function, not to be called directly
 Function: Creates a string of params to be used in the command string
 Returns : string of params
 Args    : none

_write_phylip_align_file

 Title   : _write_phylip_align_file
 Usage   : obj->__write_phylip_align_file($aln)
 Function: Internal (not to be used directly)

           Writes the alignment into the tmp directory
           in PHYLIP interlieved format

 Returns : filename
 Args    : Bio::Align::AlignI