NAME
Bio::BPWrapper::TreeManipulations - Functions for biotree
SYNOPSIS
use Bio::BPWrapper::TreeManipulations;
# Set options hash ...
initialize(\%opts);
write_out(\%opts);SUBROUTINES
initialize()
Sets up most of the actions to be performed on an alignment.
Call this right after setting up an options hash.
Sets package variables: $in_format, @nodes, $tree, $out_format, and $out.
countOTU()
Print total number of OTUs (leaves).
reroot()
Reroot tree to node in $opts{'reroot'} by creating new branch.
bin()
Divides tree into number of specified segments and counts branches up to height the segment. Prints: bin_number, branch_count, bin_floor, bin_ceiling.
write_out()
Performs the bulk of the actions actions set via initialize(\%opts).
Call this after calling #initialize(\%opts).
SEE ALSO
bioatree: command-line tool for tree manipulations
CONTRIBUTORS
William McCaig <wmccaig at gmail dot com>
Girish Ramrattan <gramratt at gmail dot com>
Che Martin <che dot l dot martin at gmail dot com>
Yözen Hernández yzhernand at gmail dot com
Levy Vargas <levy dot vargas at gmail dot com>
Weigang Qiu (Maintainer)
Rocky Bernstein