v1.4.4

• Fixing the tests script to work on bioconda and locally
• Added some checking of the input species tree for polytomies and rootedness

v1.4.3

Improved and refactored the --tests implementation for bioconda

v1.4.2

Added more descriptive messages for filtered gene trees.

v1.4.1

Fixes a bug when reading a MUL-tree with --multree.

v1.4.0

This release includes commits that:

• Hybrid tip labels now have '+' added to them in the dup-counts output
• Re-factored code
• Removed -d and replaced with the --st-only and --no-st options, which seems clearer
• Clarified how -v works
• Converted underscores in output files to hyphens
• Changed format of output files (see website: https://gwct.github.io/grampa/readme.html)
• Added -scores.txt that contains score information for all MUL-trees rather than just putting that in the .log file
• Converted global vars into a dict

GRAMPA v1.3.1

GRAMPA v1.3.1 doesn't add any major functionality, but adds warnings to the documentation that gene trees containing polytomies will be filtered from all analyses.

Install instructions: No install necessary. Simply extract to your desired location and run as python grampa.py. You may want to add the GRAMPA folder to your $PATH variable for ease of use.

See the website for more info!

GRAMPA v1.3

GRAMPA v1.3 doesn't add any major functionality, but provides a much needed clean-up of some of the code as well as some useful minor features.

• Added the --numtrees option to quickly calculate the number of MUL-trees possible for a given input.
• Added the --version option to quickly print out the version info.
• Implemented error checking for the psutil module when --stats is used.
• General upkeep.

Important note: Going forward, only Python 3+ will be supported. If you have any questions about this please let me know!

Install instructions: No install necessary. Simply extract to your desired location and run as python grampa.py. You may want to add the GRAMPA folder to your $PATH variable for ease of use.

See the website for more info!