Scripts for file processing and analysis in phylogenomics & phylogeography

PIrANHA

PIrANHA provides a set of tools for automating file processing and analysis steps in the (phylo*=) fields of phylogenomics and phylogeography (including population genomics). PIrANHA is fully command line-based and contains a series of functions for automating tasks during evolutionary analyses of genetic data.

A variety of functions manipulate DNA sequence alignments, while others conduct custom analysis pipelines; for example, one set conducts reference-based assembly, allele phasing, and alignment of allelic sequences, starting from cleaned targeted sequence capture reads. Many functions are wrappers around existing software, allowing for straightforward automation of common analysis steps in evolutionary genetics. PIrANHA is under development (join in!), but the alpha release is now stable!

New features include tab completion of function names, as follows:

INSTALL & DOCUMENTATION

Homebrew install

See here.

brew tap justincbagley/homebrew-tap ;
brew install piranha ;
source /usr/local/Cellar/piranha/*/bin/source_piranha_compl.sh ;
source ~/.bash_profile ;

For additional information on this distribution, including overview, dependencies, installation, updating, usage, workflows, etc., please see the documentation given in the Quick Guide (here or here) and the PIrANHA wiki!!!

LICENSE

All code within PIrANHA v0.4a4 repository is available "AS IS" under a 3-Clause BSD license. See the LICENSE file for more information.

CITATION

Should you cite PIrANHA? See https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md.

If you use scripts from this repository as part of your published research, please cite the repository as follows (also see DOI information below):

• Bagley, J.C. 2020. PIrANHA v0.4a4. GitHub repository, Available at: http://github.com/justincbagley/PIrANHA.

Alternatively, provide the following link to this software repository in your manuscript:

• https://github.com/justincbagley/PIrANHA

DOI

The DOI for PIrANHA, via Zenodo (also indexed by OpenAIRE), is as follows: . Here are some examples of citing PIrANHA using the DOI:

DOI specific to this version:

• Bagley, J.C. 2020. PIrANHA v0.4a4. GitHub package, Available at: http://doi.org/10.5281/zenodo.4331675.
• Bagley, J.C. 2020. PIrANHA. Zenodo, Available at: http://doi.org/10.5281/zenodo.4331675.

Generic DOI for all versions:

• Bagley, J.C. 2020. PIrANHA v0.4a4. GitHub package, Available at: http://doi.org/10.5281/zenodo.596766.
• Bagley, J.C. 2020. PIrANHA. Zenodo, Available at: http://doi.org/10.5281/zenodo.596766.

CONTENTS

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├── LICENSE
├── README.md
├── changeLog.md
├── piranha
├── Quick_Guide.md
├── Quick_Guide.pdf
├── assets
│   └── ...
├── bin
│   ├── README.md
│   ├── calcAlignmentPIS
│   ├── NEXUS2PHYLIP
│   ├── PHYLIP2NEXUS
│   ├── PHYLIP2FASTA
│   ├── PHYLIP2Mega
│   ├── PHYLIP2PFSubsets
│   └── ...
├── completions
│   ├── init.sh
│   ├── c.bash
│   ├── c.zsh
│   └── source_piranha_compl.sh
├── install
│   ├── README.md
│   ├── INSTALL
│   ├── brew_piranha
│   └── local_piranha
├── lib
│   ├── README.md
│   ├── setupScriptFunctions.sh
│   ├── sharedFunctions.sh
│   ├── sharedVariables.sh
│   ├── utils.sh
│   └── virtualenv.txt
├── etc
│   ├── README.md
│   ├── beast_runner_default.cfg
│   ├── dadi_runner_default.cfg
│   ├── pushover.cfg.sample
│   ├── raxml_runner.cfg
│   ├── snapp_runner.cfg
│   └── .gitignore
├── test
│   ├── test.fasta
│   ├── test.phy
│   ├── test.nex
│   └── ...
└── tmp
    └── .gitignore