2. Distribution Structure

PIrANHA has undergone a complete rewrite recently, as of v0.2+ (March 2019) through v0.4a3 (current, 2020), yielding a new directory structure shown below, as well as here or here. All scripts were reformatted and converted to functions ('function' programs) that are now located in the bin/ or bin/MAGNET-1.1.1/ subfolders of the distribution repository. Also, I wrote a new program, piranha.sh (controlled by executable piranha added during install), that is now the 'master' program and is responsible for running all of the functions.

Directory tree...

.
├── 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

(where ... = truncation)

The functions themselves are based on bash/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.

December 11, 2020 - Justin C. Bagley, Jacksonville, AL, USA

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