PIrANHA version 0.2-alpha.1

Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.2-alpha.1, 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.1 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), and 2) automating running these software programs on the user's personal machine (e.g. MAGNET pipeline and pyRAD2PartitionFinder scripts) or a remote supercomputer machine, and then conducting post-processing of the results. See full description in the README.

What's new?

v0.2-alpha.1

Since v0.2-alpha, the current pre-release version, PIrANHA v0.2-alpha.1 adds several updates including redos for the PIrANHA etc/ dir, a README for bin/, and new scripts for the MLEResultsProc, getTaxonNames, taxonCompFilter, and SNAPPRunner functions.

v0.2-alpha

Pre-release version, PIrANHA v0.2-alpha.1, involved a virtually complete rewrite and reorganization of PIrANHA (with >1,200 additions and >400 deletions). All scripts were converted to 'function' programs in bin/ or bin/MAGNET-1.0.0/ of the repo, and I wrote a new program, piranha, that is now the main program and runs all functions. I am still in the process of updating the README and all function scripts, but I decided to do a pre-release ratcheted up to v0.2 due to the great improvements in modularization and efficiency that v0.2 update allows (selecting a function and passing all arguments, all from piranha), and because I wanted a new alpha release to use as a starting point to create Debian and Homebrew distribution releases (i.e. brew tap(s) to update as new versions roll out during development). The current organization of PIrANHA is also going to be much better suited for general use, and for adding other collaborators or developers.

The changeLog.md is not yet up to date (not even for v0.2-alpha.1) and the repository is close but still not ready for a v1.0 major release, but we're getting there!!