PIrANHA version 0.4-alpha-2

Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.4a2, a software package that provides a number of utility functions and pipelines for file processing and analysis in phylogenetics, phylogenomics, and phylogeography. PIrANHA stands for "Phylogenetics and Phylogeography," and v0.4a2 (=v0.4-alpha-2) is a new development pre-release, or 'minor version' that is greatly improved and ready for alpha testing! Feel free to download this release and try it out; however, PIrANHA is still under active development. Email all suggestions and bug fix requests to Justin directly at bagleyj (at) umsl (dot) edu (also see Contact page of the wiki).

See full description in the PIrANHA README, Quick Guide, and wiki pages.

What's new?

v0.4a2 (v0.4-alpha-2)

This update builds on the previous pre-release, v0.4a, by updating the main prianha script (including improvements to messaging, function list, and help text); addition of a new phaseAlleles function that automates phasing of consensus sequences from HTS (e.g. targeted sequence capture) based on reads (re)mapped to a reference assembly FASTA file; as well as minor updates to all functions (improved messaging, minor bug fixes, and minor reformatting).