PIrANHA version 0.2-alpha.2

Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.2-alpha.2, a software package that provides a number of utility scripts and pipelines for file processing and analysis in phylogenetics and phylogeography. PIrANHA stands for "PhylogenetIcs ANd pHylogeogrAphy," and v0.2-alpha.2 is a new development pre-release, or 'minor version' that is greatly improved but not yet ready for production use.

PLEASE DO NOT DOWNLOAD THIS RELEASE. IT IS UNDER ACTIVE DEVELOPMENT

PIrANHA tools include interactive/non-interactive shell scripts and wrapper scripts focusing on (1) analyses of DNA sequence data and SNPs or RAD loci generated from massively parallel sequencing runs on reduced representation genomic libraries, e.g. from ddRAD-seq (Peterson et al. 2012) or target capture, and (2) automating running these software programs on the user's personal machine (e.g. MAGNET pipeline and pyRAD2PartitionFinder scripts) or a remote supercomputer, and then conducting post-processing of the results. See full description in the README and wiki pages.

What's new?

v0.2-alpha.2

This is a minor update to the pre-release version that adds a new FASTA2VCF function that converts a sequential FASTA multiple sequence alignment into a variant call format (VCF) file, and allows subsampling 1 SNP per partition/locus. This update also includes edits to the README, index.html, changeLog.md, and travis.yml files. Importantly, I have also now created a successful homebrew tap for PIrANHA here with a formula that is working with v0.2-alpha, and that is now described in the documentation wiki.