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

• Qiu Lab wiki page

• Github project wiki page

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