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PIrANHA version 0.3-alpha.1

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@justincbagley justincbagley released this 07 May 17:33
· 630 commits to master since this release
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Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.3a1, a software package that provides a number of utility functions and pipelines for file processing and analysis in phylogenetics and phylogeography. PIrANHA stands for "PhylogenetIcs ANd pHylogeogrAphy," and v0.3a1 (=v0.3-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 functions 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?

v0.3a1 (v0.3-alpha.1)

This minor update builds on the previous pre-release, v0.2-alpha.2, by making a variety of changes towards finalizing function rewrites and getting most or all functions working. The most recent changes include:

  • May 7, 2019: Fixed main piranha function so that it correctly reads in all arguments passed with the --args='' flag (should also work with -a), which previously caused several functions to fail and invoke trapExit.
  • April 30 – May 7, 2019: Added bug fixes and updates to dropRandomHap, PHYLIP2NEXUS, PHYLIP2FASTA, PHYLIP2Mega, and splitPHYLIP functions.
  • April 10, 2019: Added new renameTaxa function that renames taxon (sample) names in genetic data files of type FASTA, NEXUS, PHYLIP, and VCF according to user specifications.
  • April 9, 2019: Added updated scripts to fix bugs in FASTA2PHYLIP and getTaxonNames functions.