Outgroup Analysis Resources

This web page makes additional files available for the outgroup analysis based scoring method presented in:

A Schneider and GM Cannarozzi (2009): Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal, Molecular Biology and Evolution 26(6): 1259–1272.

Python script to compute outgroup score

We created a Python script to compute the outgroup score from a table of gene tree support using different outgroups. The script requires the NumPy package.

Python script: outgroups.py
Example input file: example.txt

The example input file contains the example presented in Table 1 of the article, the analysis of the human, mouse, rabbit phylogeny using six outgroups.
The follwing command runs the example:

python outgroups.py example.txt

The script accepts one or more file names as arguments and processes them all. It contains a variable verbose which, when set to true, makes the script output more information. If set to false, it will only produce a minimal output.