2. Distribution Structure

PIrANHA has undergone a complete rewrite recently, as of v0.2+ (March 2019), yielding a new directory structure shown below, as well as here or here. All scripts were reformatted and converted to 'function' programs in bin/ or bin/MAGNET-1.1.0/ of the repository, and I wrote a new program, piranha, that is now the 'master' program and is responsible for running all functions.

Directory tree...

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

The functions themselves are based on shell scripts and R scripts that were originally written by the author, as well as additional R, Perl, and Python scripts brought in from other authors. Details and attributions are given where warranted in the Acknowledgements section of the Introduction, and also throughout READMEs, scripts, and usage texts of files in the repo.

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