AfterPhylo

a Perl script for manipulating trees after phylogenetic reconstruction

Version 0.9.1

by Qiyun Zhu (qiyunzhu@gmail.com)

Features

• Annotate tips (IDs -> full taxa names).
• Compute average confidence value across tree.
• Scale up/down branch lengths.
• Remove branch lengths and keep topology only.
• Collapse nodes with confidence values lower than a cutoff.
• Convert between Newick and Nexus formats, with confidence values kept.
• Compatible with trees generated by RAxML, PhyML, MrBayes, BEAST or other popular phylogenetics programs.

Usage

perl AfterPhylo.pl [options(s)] [tree(s)]

Input:

One or more trees in Newick or Nexus format.

Options:

• -format=<newick or nexus>

  Convert tree format to Newick or Nexus.

• -annotate=<annotation table>

  Annotate tree tips (append a string to each tip label)

  Annotation table format: plain text file with each line like ID<tab>name.

• -replace

  When annotating, ignore ID instead of appending (must be used with -annotate).

• -scale=<factor>

  Scale up/down branch lengths by <factor>.

• -topology

  Remove branch lengths (keep topology only).

• -unlabeled

  Remove node labels (confidence values or everything in brackets).

• -confonly

  Keep confidence values (bootstrap, posterior probability, etc) and remove everything else from complicated node labels.

• -average

  Compute average confidence value across tree.

• -collapse=<number>

  Collapse nodes with confidence value below <number>.

• -simplify

  Simplify branch length values to six digits after decimal point.

Examples

Convert three MrBayes consensus trees into Newick format with posterior probabilities as node labels:

perl AfterPhylo.pl -confonly -format=newick tree1.nex tree2.nex tree3.nex

Prepare a starting tree for divergence time estimation in BEAST, with root height expanded from 1.0 to in 65 (Ma):

perl AfterPhylo.pl -scale=65 -format=nexus tree1.nwk

Compute the average bootstrap values of a tree:

perl AfterPhylo.pl -average tree1.nwk

Create a majority-rule consensus tree from an "all" tree:

perl AfterPhylo.pl -collapse=50 tree1.nwk

Replace tip labels with full taxa names

perl AfterPhylo.pl -annotate=translation_table.txt -replace tree1.nex

The file translation_table.txt looks like:

HUMAN   Homo sapiens
CHIMP   Pan troglodytes
GORIL   Gorilla gorilla
...

Dependencies

This program does not depend on any third-party modules.

License

Licensed under the BSD 2-clause license.