PIrANHA version 0.2-alpha

Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.2-alpha, a software package that provides a number of utility scripts and pipelines for file processing and analysis in phylogenetics and phylogeography. PIrANHA stands for "PhylogenetIcs ANd pHylogeogrAphy," and v0.2-alpha 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 shell scripts and 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), 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. See full description in the README.

What's new?

The current pre-release version, PIrANHA v0.2-alpha, involved a virtually complete rewrite and reorganization of PIrANHA (with >1,200 additions and >400 deletions). All scripts were converted to 'function' programs in bin/ or bin/MAGNET-1.0.0/ of the repo, and I have written a new program, piranha, that is now the main program and runs all functions. I am still in the process of updating the README and all function scripts, but I am doing a pre-release ratcheted up to v0.2 due to the great improvements in modularization and efficiency that this update allows (selecting a function and passing all arguments, all from piranha), and because I want a new release to use as a starting point to create Debian and Homebrew distribution releases (i.e. brew tap(s) to update as new versions roll out during development). The current organization of PIrANHA is also going to be much better suited for general use, and for adding other collaborators or developers.

The changeLog.md is not yet up to date (not even for v0.2-alpha) and the repository is close but still not ready for a v1.0 major release, but we're getting there!!

PIrANHA version 0.1.7

Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.1.7, a software package that provides a number of utility scripts and pipelines for file processing and analysis in phylogenetics and phylogeography. PIrANHA stands for "PhylogenetIcs ANd pHylogeogrAphy," and v0.1.7 is a new development release, or 'minor version'.

PIrANHA tools include interactive/non-interactive shell scripts and 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), 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. See full description in the README.

What's new?

The current release, PIrANHA v0.1.7, updates the README and several scripts in this software package, as described in changeLog.md.

PIrANHA version 0.1.6.1

Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.1.6.1, a new development release (minor version, partly stable and partly unstable) 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?

The current release, PIrANHA v0.1.6.1, updates the README and documentation for the repository.

PIrANHA version 0.1.6

Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA (PhylogenetIcs ANd pHylogeogrAphy) v0.1.6, a new development release (minor version, partly stable and partly unstable) of PIrANHA that provides a number of utility scripts and pipelines for file processing and analysis in 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: + updated all README files in the repository (for PIrANHA, BEASTPostProc, BEASTRunner, ExaBayesPostProc, MLEResultsProc, and fastSTRUCTURE scripts).
• August 2017: + added new 'BEASTReset.sh' script, and corresponding README, into BEASTReset sub-folder. This script automates re-setting random starting number seeds in BEAST run submission scripts for supercomputer runs. This is a time-saving script when many failed runs need to be restarted from a different seed!
• bug fix: - MLEResultsProc.sh (expands capability of detecting and accounting for PS/SS runs conducted in different versions of BEAST, i.e. v1 vs. v2)
• bug fix: - PFSubsetSum.sh (fixes incorrect ordering of summary statistics)
• bug fix: - PFSubsetSum.sh (fixed script so that it works with PartitionFinder v1 and v2; last testing: v2.1.1)

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

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!

PIrANHA version 0.1.3

PIrANHA v0.1.3

This is a PIrANHA v0.1.3, a new development release version that is still in active development. PIrANHA stands for "PhylogenetIcs ANd pHylogeogrAphy" and includes a number of utilities and pipelines for file processing and analysis in phylogenetics and phylogeography, including the latest release of the MAGNET repository pipeline, v0.1.3 (https://github.com/justincbagley/MAGNET/).

What's new?

This version of PIrANHA introduces the BEASTRunner.sh script for automating independent runs of BEAST1 or BEAST2 on a remote supercomputing cluster. See README for details.

PIrANHA version 0.1.2

PIrANHA v0.1.2

This is a PIrANHA v0.1.2, a new development release version that is still in active development. PIrANHA stands for "PhylogenetIcs ANd pHylogeogrAphy" and includes a number of utilities and pipelines for file processing and analysis in phylogenetics and phylogeography, including the latest release of the MAGNET repository pipeline, v0.1.3 (https://github.com/justincbagley/MAGNET/).

PIrANHA version 0.1.1

PIrANHA v0.1.1

This is a PIrANHA v0.1.1, an early development release version that is still in active development. PIrANHA stands for "PhylogenetIcs ANd pHylogeogrAphy" and includes a number of utilities and pipelines for file processing and analysis in phylogenetics and phylogeography, including the latest release of the MAGNET repository pipeline, v0.1.2 (https://github.com/justincbagley/MAGNET/).

PIrANHA major version 0

PIrANHA v0.1.0

This is PIrANHA v0.1.0, major version zero for initial development. PIrANHA stands for "PhylogenetIcs ANd pHylogeogrAphy" and includes a number of utilities and pipelines for file processing and analysis in phylogenetics and phylogeography, including the latest release of the MAGNET repository pipeline, v0.1.1 (https://github.com/justincbagley/MAGNET/). PIrANHA is first being released to the public as v0 (and not a beta version) because its scripts run out of the box, with no bugs. However, this is an 0.1 release because this software is in development, and new minor additions and fixes may be added soon, before a major version 1 release.