PIrANHA version 0.2-alpha.1c

Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.2-alpha.1c, 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.1c 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.1c

This is a minor update to the pre-release version that includes edits to the README and index.html files, and that adds this slightly updated changeLog.md file back into the repository. Other changes include removing bin/trash function due to conflicts with /usr/local/bin/trash symlink belonging to trash on macOS, which caused homebrew install to fail. After fixing this, I have also now created a successful homebrew tap for PIrANHA that is working with this release (more info soon, to be added to the README).

v0.2-alpha.1b

This is a very minor update to the pre-release version removing some PHYLIP and FASTA DNA sequence alignments that I had previously included in the repo for my own testing purposes, and updating README and index.html files.

v0.2-alpha.1

Since v0.2-alpha, the pre-release version of PIrANHA v0.2-alpha.1 added 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. (See more on v0.2 changes in v0.2 and v0.2-alpha release notes below.)