PIrANHA version 0.1.5

Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.1.5, 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." PIrANHA tools are largely interactive shell scripts focusing on 1) analyses of DNA sequence data and SNPs or RAD 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?

• August 2017: + added a Change Log file ('changeLog.md') to supplement releases page and provide log file within master.
• August 2017: + updated MAGNET pipeline by editing 'MAGNET.sh' by adding three new command line options ("-e", "-m", and "-o" flags), as follows:
  -e executable (def: raxmlHPC-SSE3) name of RAxML executable, accessible from command line
  on user's machine
  -m indivMissingData (def: 1=allowed; 0=removed)
  -o outgroup (def: NULL) outgroup given as single taxon name (tip label) or comma-
  separted list
• August 2017: + updated MAGNET pipeline by adding 'getBootTrees.sh' script, which collates and organizes bootstrap trees from all RAxML runs in sub-folders of a working directory, especially results of a MAGNET run. This is the standalone version of the script.
• August 2017: + updated 'BEASTPostProc.sh'
• August 2017: + updated 'BEASTRunner.sh'
• August 2017: + updated 'BEAST_PSPrepper.sh' script automating editing existing BEAST v2+ (e.g. v2.4.5) input XML files for path sampling analysis, so that users don't have to do this by hand!
• bug fix: - MAGNET.sh (unused code)
• bug fix: - getGeneTrees.sh (unused code)
• bug fix: - BEASTRunner.sh