A python script for branch-site positive-selection analysis

Requirement

• Python >= 2.7 (3.x is recommended)
• ETE3 package

Usage

You can get a summary of available command-line options with branch_site_pipeline.py -h

$ python branch_site_pipeline.py -h
usage: branch_site_pipeline.py [-h] [-i INPUT_FILE] [-o OUTPUT_DIR] [-v]
                               [-l LOGFILE] [-t THREADS]
[...]

Input

You need to prepare a text file including these information:

1. cDNA alignment file (*.fasta, *.paml);
2. tree file (newick format);
3. Any specific nodes in the tree. (Cautions: all nodes need to be monophyletic). If you want to test all branches, just leave blank here.

Note: test.txt in the source package is an example input file.

Output

Two files will be output in the output directory:

1. all_results.txt including all calculation results and nodes diagrams;
2. positive_selection_tree.png showing all nodes with positive selection.