PIrANHA version 0.4-alpha-3

Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.4a3, 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 v0.4a3 (=v0.4-alpha-3) 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?

v0.4a3 (v0.4-alpha-3)

This update builds on the previous pre-release, v0.4a2, by adding minor bug fixes and improvements to several functions. With the addition of the new function alignAlleles, a companion script meant to be run directly after phaseAlleles, this release establishes a new workflow for phasing and aligning consensus sequences from HTS (e.g. targeted sequence capture data) based on reads (re)mapped to a reference assembly FASTA file (i.e. following reference-based assembly). This combination of programs was designed to be run on target capture data after first conducting cleaning, assembly, locus selection, and reference-based assembly (specifically created with SECAPR (Andermann et al. 2018) in mind, and tested using output from SECAPR).

Additionally, this update introduces several other new functions. These include a new trimSeqs for trimming DNA sequences in PHYLIP alignments, with custom gap handling options in trimAl, and outputting trimmed results files in FASTA, PHYLIP, or NEXUS formats. There is a geneCounter function that counts and summarizes number of gene copies per tip taxon label in a set of input gene trees in Newick format, given a taxon-species assignment file (this function written to handle output from HybPiper pipeline; see Usage text). And I've also added a new batchRunFolders function that automates splitting a set of input files into different batches (to be run in parallel on a remote supercomputing cluster, or a local machine), starting from file type or list of input files; specifically, this function allows you to prep batch analyses in MAFFT, RAxML, and IQ-TREE.