PIrANHA version 0.1.4

Scripts for file processing and analysis in phylogenomics & phylogeography

This is a PIrANHA v0.1.4, a new development release version of PIrANHA that provides a number of utility scripts and pipelines for file processing and analysis in phylogenetics and phylogeography. PIrANHA stands for "PhylogenetIcs ANd pHylogeogrAphy." The current code in PIrANHA has been written to largely focus on 1) analyses of DNA sequence data and SNPs or SNP loci generated from massively parallel sequencing runs on ddRAD-seq genomic libraries (e.g. 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.

What's new?

• May 2017: build now contains new BEASTRunner.sh script and 'beast_runner.cfg' configuration file. BEASTRunner now has options to allow specifying 1) number of runs, 2) walltime, and 3) Java memory allocation per run, as well as calling reg or verbose help documentation from the command line.
• April 2017: build now contains new pyRADLocusVarSites.sh script (with example run folder) that calculates numbers of variable sites (i.e. segregating sites, S) and parsimony-informative sites (PIS; i.e. hence with utility for phylogenetic analysis) in each SNP locus contained in .loci file from a pyRAD assembly run.
• April 2017: I added new dadiRunner.sh script that automates transferring and queuing multiple runs of dadi input files on a remote supercomputer (similar to BEASTRunner and RAxMLRunner scripts already in the repo). n.b.: A dadiPostProc.sh script is also in the works (but unreleased) that conducts post-processing and graphical plotting of results from multiple dadi runs
• January 2017: I added a new script called BEAST_PSPrepper.sh that, while not quite polished, automates editing any existing BEAST v2+ (e.g. v2.4.4) input XML files for path sampling analysis, so that users don't have to do this by hand!