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.\" ========================================================================
.\"
.IX Title "Bio::TreeIO::nexus 3pm"
.TH Bio::TreeIO::nexus 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::TreeIO::nexus \- A TreeIO driver module for parsing Nexus tree output from PAUP
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 4
\&  use Bio::TreeIO;
\&  my $in = Bio::TreeIO\->new(\-file => \*(Aqt/data/cat_tre.tre\*(Aq);
\&  while( my $tree = $in\->next_tree ) {
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a driver module for parsing \s-1PAUP\s0 Nexus tree format which
basically is just a remapping of trees.
.SS "Comments"
.IX Subsection "Comments"
The nexus format allows node comments that are placed inside square
brackets. Usually the comments (implemented as tags for nodes) are
used to give a name for an internal node or record the bootstrap value,
but other uses are possible.
.PP
The FigTree program by Andrew Rambaut adds various rendering
parameters inside comments and flags these comments by starting them
with '&!'. The parameters implemented here are 'label' and 'color'.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason-at-open-bio-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Args    : \-header    => boolean  default is true 
\&                         print/do not print #NEXUS header
\&           \-translate => boolean default is true
\&                         print/do not print Node Id translation to a number
.Ve
.SS "next_tree"
.IX Subsection "next_tree"
.Vb 5
\& Title   : next_tree
\& Usage   : my $tree = $treeio\->next_tree
\& Function: Gets the next tree in the stream
\& Returns : Bio::Tree::TreeI
\& Args    : none
.Ve
.SS "write_tree"
.IX Subsection "write_tree"
.Vb 5
\& Title   : write_tree
\& Usage   : $treeio\->write_tree($tree);
\& Function: Writes a tree onto the stream
\& Returns : none
\& Args    : Bio::Tree::TreeI
.Ve
.SS "header"
.IX Subsection "header"
.Vb 6
\& Title   : header
\& Usage   : $obj\->header($newval)
\& Function: 
\& Example : 
\& Returns : value of header (a scalar)
\& Args    : on set, new value (a scalar or undef, optional)
.Ve
.SS "translate_node"
.IX Subsection "translate_node"
.Vb 6
\& Title   : translate_node
\& Usage   : $obj\->translate_node($newval)
\& Function: 
\& Example : 
\& Returns : value of translate_node (a scalar)
\& Args    : on set, new value (a scalar or undef, optional)
.Ve