Scripts for file processing and analysis in phylogenomics & phylogeography
All code within PIrANHA v0.4a2 repository is available "AS IS" under a 3-Clause BSD license. See the LICENSE file for more information.
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 v0.4a2. GitHub repository, Available at: http://github.com/justincbagley/PIrANHA.
Alternatively, provide the following link to this software repository in your manuscript:
The DOI for PIrANHA, via Zenodo (also indexed by OpenAIRE), is as follows: . Here are some examples of citing PIrANHA using the DOI:
Bagley, J.C. 2020. PIrANHA v0.4a2. 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.
For additional information on this distribution, including overview, dependencies, installation, updating, usage, workflows, etc., please see the documentation given in the Quick Guide and the PIrANHA wiki!!!
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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