svr_cohesion_groups

    svr_cohesion_groups [options] < tree.newick > cohesion_groups.table

This script classifies tips of a newick tree into cohesion groups based on bootstrap values of tree branches.

Introduction

A cohesion group is a collection of protein sequences from various organisms whose amino acid sequences assemble as a compact cluster on a phylogenetic tree.

See Roy A. Jensen's cohesion group analysis (PubMed ID: 18322033)

Command-line options

-c bootstrap_cutoff

Specifies the threshold of branch support value for collapsing subtrees. (D = 0.85)

-f max_CG_size_in_fraction

Max fraction of a cohesion group (D = 0.20).

-m max_CG_size

Max size of a cohesion group (D = number of tips in tree).

-o

With the -o option, all orphan cohesion groups are labeled as 'Orp'.

Input

The input tree is a newick file read from STDIN.

Output

The output is a two-column table [ tip_id, cohesion_group_id ] written to STDOUT.