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PIrANHA version 0.3-alpha.2

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@justincbagley justincbagley released this 26 Jul 19:17
· 593 commits to master since this release
v0.3a2
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Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.3a2, 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 v0.3a2 (=v0.3-alpha.2) is a new development pre-release, or 'minor version' that is greatly improved and ready for alpha testing! Please feel free to download this release and try it out, as most of the scripts have been verified; however, realize that PIrANHA is still under active development. Please 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 and wiki pages.

What's new?

v0.3a2 (v0.3-alpha.2)

This update builds on the previous pre-release, v0.3-alpha.1, by adding new functions, rewriting others, and adding updates and bug fixes. The most recent changes include:

PIrANHA v0.3a2 (official minor pre-release version 0.3-alpha.2) - July 26, 2019

  • July 26, 2019: Updated README, repository files, and wiki files for new release.
  • July 25, 2019: Added new RogueNaRokRunner function that reads in a Newick-formatted tree file and runs it through RogueNaRok to identify rogue taxa. Additionally, I conducted a complete rewrite of the NEXUS2PHYLIP function that removes its dependence on N. Takebayashi's Perl script (see previous version, Acknowledgements), and I made minor edits to piranha and edits and bug fixes for other functions including RYcoder.
  • July 24, 2019: Minor updates and bug fixes for PHYLIP2NEXUS function.
  • July 11, 2019: Minor updates and fixes for PHYLIP2Mega function.
  • June 11, 2019: Added new RYcoder function that reads in a PHYLIP or NEXUS DNA sequence alignment and converts it into 'RY'-coded, binary format, with purines (A, G) coded as 0's and pyrimidines (C, T) coded as 1's.
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