Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


Bio::AlignIO::phylip - PHYLIP format sequence input/output stream


# Do not use this module directly. Use it via the Bio::AlignIO class.
     use Bio::AlignIO;
     use Bio::SimpleAlign;
     #you can set the name length to something other than the default 10
     #if you use a version of phylip (hacked) that accepts ids > 10
     my $phylipstream = Bio::AlignIO->new(-format  => 'phylip',
                                         -fh      => \*STDOUT,
     # convert data from one format to another
     my $gcgstream     =  Bio::AlignIO->new(-format => 'msf',
                                           -file   => 't/data/cysprot1a.msf');
     while( my $aln = $gcgstream->next_aln ) {
     # do it again with phylip sequential format format
     # can also initialize the object like this
     $phylipstream = Bio::AlignIO->new(-interleaved => 0,
                                      -format => 'phylip',
                                      -fh   => \*STDOUT,
     $gcgstream     =  Bio::AlignIO->new(-format => 'msf',
                                        -file   => 't/data/cysprot1a.msf');
     while( my $aln = $gcgstream->next_aln ) {


This object can transform Bio::SimpleAlign objects to and from PHYLIP fotmat. By deafult it works with the interleaved format. By specifying the flag -interleaved => 0 in the initialization the module can read or write data in sequential format.

Long IDs up to 50 characters are supported by flag -longid => 1. ID strings can be surrounded by single quoted. They are mandatory only if the IDs contain spaces.



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

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 the bugs and their resolution. Bug reports can be submitted via the web:

AUTHORS - Heikki Lehvaslaiho and Jason Stajich

Email: heikki at Email: jason at


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


  Title   : new
  Usage   : my $alignio = Bio::AlignIO->new(-format => 'phylip'
                                           -file   => '>file',
                                           -idlength => 10,
                                           -idlinebreak => 1);
  Function: Initialize a new L<Bio::AlignIO::phylip> reader or writer
  Returns : L<Bio::AlignIO> object
  Args    : [specific for writing of phylip format files]
            -idlength => integer - length of the id (will pad w/
                                                     spaces if needed)
            -interleaved => boolean - whether interleaved
                                      or sequential format required
            -line_length  => integer of how long a sequence lines should be
            -idlinebreak => insert a line break after the sequence id
                            so that sequence starts on the next line
            -flag_SI => whether or not write a "S" or "I" just after
                        the num.seq. and line len., in the first line
            -tag_length => integer of how long the tags have to be in
                          each line between the space separator. set it
                          to 0 to have 1 tag only.
            -wrap_sequential => boolean for whether or not sequential
                                    format should be broken up or a single line
                                    default is false (single line)
            -longid => boolean for allowing arbitrary long IDs (default is false)


  Title   : next_aln
  Usage   : $aln = $stream->next_aln()
  Function: returns the next alignment in the stream.
            Throws an exception if trying to read in PHYLIP
            sequential format.
  Returns : L<Bio::SimpleAlign> object
  Args    :


  Title   : write_aln
  Usage   : $stream->write_aln(@aln)
  Function: writes the $aln object into the stream in MSF format
  Returns : 1 for success and 0 for error
  Args    : L<Bio::Align::AlignI> object


  Title   : interleaved
  Usage   : my $interleaved = $obj->interleaved
  Function: Get/Set Interleaved status
  Returns : boolean
  Args    : boolean


  Title   : flag_SI
  Usage   : my $flag = $obj->flag_SI
  Function: Get/Set if the Sequential/Interleaved flag has to be shown
            after the number of sequences and sequence length
  Example :
  Returns : boolean
  Args    : boolean


  Title   : idlength
  Usage   : my $idlength = $obj->idlength
  Function: Get/Set value of id length
  Returns : string
  Args    : string


  Title   : line_length
  Usage   : $obj->line_length($newval)
  Returns : value of line_length
  Args    : newvalue (optional)


  Title   : tag_length
  Usage   : $obj->tag_length($newval)
  Example : my $tag_length = $obj->tag_length
  Returns : value of the length for each space-separated tag in a line
  Args    : newvalue (optional) - set to zero to have one tag per line


  Title   : id_linebreak
  Usage   : $obj->id_linebreak($newval)
  Returns : value of id_linebreak
  Args    : newvalue (optional)


  Title   : wrap_sequential
  Usage   : $obj->wrap_sequential($newval)
  Returns : value of wrap_sequential
  Args    : newvalue (optional)


  Title   : longid
  Usage   : $obj->longid($newval)
  Returns : value of longid
  Args    : newvalue (optional)