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README.md

Codacy Badge License

Scripts for file processing and analysis in phylogenomics & phylogeography

LICENSE

All code within PIrANHA v0.4a3 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):

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

DOI

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

Bagley, J.C. 2020. PIrANHA v0.4a3. 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.

DOCUMENTATION

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!!!

CONTENTS

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├── LICENSE
├── README.md
├── changeLog.md
├── piranha
├── Quick_Guide.md
├── Quick_Guide.pdf
├── bin
│   ├── README.md
│   ├── calcAlignmentPIS
│   ├── NEXUS2PHYLIP
│   ├── PHYLIP2NEXUS
│   ├── PHYLIP2FASTA
│   ├── PHYLIP2Mega
│   ├── PHYLIP2PFSubsets
│   └── ...
├── 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
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