.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.16) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. 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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::TreeIO::newick \- TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 5 \& # do not use this module directly \& use Bio::TreeIO; \& my $treeio = Bio::TreeIO\->new(\-format => \*(Aqnewick\*(Aq, \& \-file => \*(Aqt/data/LOAD_Ccd1.dnd\*(Aq); \& my $tree = $treeio\->next_tree; .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This module handles parsing and writing of Newick/PHYLIP/New Hampshire format. .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://redmine.open\-bio.org/projects/bioperl/ .Ve .SH "AUTHOR \- Jason Stajich" .IX Header "AUTHOR - Jason Stajich" Email jason-at-bioperl-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 6 \& Title : new \& Args : \-print_count => boolean default is false \& \-bootstrap_style => set the bootstrap style (one of nobranchlength, \& molphy, traditional) \& \-order_by => set the order by sort method \& (see L ) .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 : L \& Args : none .Ve .SS "write_tree" .IX Subsection "write_tree" .Vb 5 \& Title : write_tree \& Usage : $treeio\->write_tree($tree); \& Function: Write a tree out to data stream in newick/phylip format \& Returns : none \& Args : L object .Ve .SS "print_tree_count" .IX Subsection "print_tree_count" .Vb 5 \& Title : print_tree_count \& Usage : $obj\->print_tree_count($newval) \& Function: Get/Set flag for printing out the tree count (paml,protml way) \& Returns : value of print_tree_count (a scalar) \& Args : on set, new value (a scalar or undef, optional) .Ve .SS "bootstrap_style" .IX Subsection "bootstrap_style" .Vb 7 \& Title : bootstrap_style \& Usage : $obj\->bootstrap_style($newval) \& Function: A description of how bootstraps and branch lengths are \& written, as the ID part of the internal node or else in [] \& in the branch length (Molphy\-like; I am sure there is a \& better name for this but am not sure where to go for some \& sort of format documentation) \& \& If no branch lengths are requested then no bootstraps are usually \& written (unless someone REALLY wants this functionality...) \& \& Can take on strings which contain the possible values of \& \*(Aqnobranchlength\*(Aq \-\-> don\*(Aqt draw any branch lengths \- this \& is helpful if you don\*(Aqt want to have to \& go through and delete branch len on all nodes \& \*(Aqmolphy\*(Aq \-\-> draw bootstraps (100) like \& (A:0.11,B:0.22):0.33[100]; \& \*(Aqtraditional\*(Aq \-\-> draw bootstraps (100) like \& (A:0.11,B:0.22)100:0.33; \& Returns : value of bootstrap_style (a scalar) \& Args : on set, new value (a scalar or undef, optional) .Ve .SS "order_by" .IX Subsection "order_by" .Vb 6 \& Title : order_by \& Usage : $obj\->order_by($newval) \& Function: Allow node order to be specified (typically "alpha") \& See L \& Returns : value of order_by (a scalar) \& Args : on set, new value (a scalar or undef, optional) .Ve