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Justin C. Bagley edited this page Dec 18, 2020 · 60 revisions

Phylo* File Processing and Automation Using PIrANHA

Quick Guide for the Impatient

PIrANHA provides a set of tools for automating file processing and analysis in (phylo*=) phylogenetics, phylogenomics, and phylogeography.

NOTE: By convention, in all content we refer to this software package as "PIrANHA" and we write the name of the main script in the package as piranha.

Downloading, installing, and upgrading PIrANHA (on macOS or Linux) is easy thanks to Homebrew distribution.

Homebrew install

See here.

Two Homebrew Install Options:

Recommended:

  1. Development (cutting edge) Homebrew install 'by-hand':
# Install:
brew tap justincbagley/homebrew-tap ;
brew update ;
brew install --HEAD piranha ;
piranha -i ;
  1. Regular Homebrew install 'by-hand' (stable, but may not be up to date):
# Install:
brew tap justincbagley/homebrew-tap ;
brew update ;
brew install piranha ;

After running one of the installs above, it is recommended that users do source ~/.bash_profile next on macOS, or source ~/.bashrc next on Linux. To ensure PIrANHA install success, or if piranha executable is not available with dynamnic tab completion (shown here) at the command line interface (CLI), then do:

source /usr/local/Cellar/piranha/*/bin/source_piranha_compl.sh ;
source ~/.bash_profile ;

Updating PIrANHA

Recommended:

  1. Upgrading to development (cutting edge) version:
brew upgrade --fetch-HEAD piranha ;
piranha -i ;

Help

Get the help text and a list of functions available in PIrANHA like so (notice <TAB> for dynamic completion):

piranha -h
piranha -f <TAB>
piranha -f list
piranha -s|--shortlist

Get the help text for a particular function:

piranha -f <function> -h

Example usage

Convert between DNA alignment formats like so:

# Convert FASTA to PHYLIP:

    piranha -f FASTA2PHYLIP -f 1 -i <inputFASTA> -k 1 -v 1     # Single PHYLIP file
    piranha -f FASTA2PHYLIP -f 2 -k 1 -v 1                     # Multiple PHYLIP files

# Convert FASTA to VCF:

    piranha -f FASTA2VCF -i <inputFASTA> -o <output>

# Convert Mega to PHYLIP:

    piranha -f Mega2PHYLIP -i <inputMega> -k 1                  # Single Mega file
    piranha -f Mega2PHYLIP -m 1 -k 1                            # Multiple Mega files
# Convert NEXUS to PHYLIP:

    piranha -f NEXUS2PHYLIP -i <inputNEXUS> -v 1                # Single NEXUS file

# Convert PHYLIP to FASTA:

    piranha -f PHYLIP2FASTA -i <inputPHYLIP> -k 1              # Single FASTA file
    piranha -f PHYLIP2FASTA -m 1 -k 1 -v 1                     # Multiple FASTA files 

# Convert PHYLIP to Mega:

    piranha -f PHYLIP2Mega -i <inputPHYLIP> -k 1               # Single PHYLIP file
    piranha -f PHYLIP2Mega -m1 -k 1                            # Multiple PHYLIP files

# Convert PHYLIP to NEXUS:

    piranha -f PHYLIP2NEXUS -i <inputPHYLIP> -p <partitionsFile> -f NEX     # Single PHYLIP file 
    piranha -f PHYLIP2NEXUS -m 1                                            # Multiple PHYLIP files

Concatenate DNA sequence alignments (e.g. genes) like so:

# Create <taxonNamesSpaces> file with getTaxonNames function (creates file '<numTips>_taxon_names_spaces.txt'):

    piranha -f getTaxonNames -n <numTips>

# Concatenate PHYLIP alignments (e.g. 1 per gene):

    piranha -f concatenateSeqs -t <numTips>_taxon_names_spaces.txt

# Complete (fill in missing individuals) and concatenate PHYLIP alignments: 

    piranha -f completeConcatSeqs -t <numTips>_taxon_names_spaces.txt

Trim DNA sequence alignments like so:

# Use trimSeqs to trim single PHYLIP alignment with default settings and PHYLIP output:

     piranha -f trimSeqs -i <inputPHYLIP> -o phylip
     piranha -f trimSeqs --input <inputPHYLIP> --output phylip

# Use trimSeqs to trim multiple PHYLIP alignments with default settings and PHYLIP output:

     piranha -f trimSeqs -m 1 -o phylip
     piranha -f trimSeqs --multi 1 --output phylip

# Use trimSeqs to trim PHYLIP alignments with custom gap handling and sequence conservation settings for trimAl:

     piranha -f trimSeqs --multi 1 --output phylip --cons 60 --gt 0.1

# Use trimSeqs to trim PHYLIP alignments stringently, removing all sites with gaps:

     piranha -f trimSeqs --multi 1 --output phylip --nogaps 1

# NOTE: You may also switch output formats to FASTA (--output fasta) or NEXUS (--output nexus) formats.

Phase consensus sequences from HTS (e.g. targeted sequence capture) using reference:

# Phase alleles with default settings (creates intermediate files and final, unaligned phased FASTAs):

    piranha -f phaseAlleles -i <input> -o <output> -r <reference>

# Phase alleles while masking reference indels (insertions/deletions) in final, unaligned phased FASTAs:

    piranha -f phaseAlleles -i <input> -o <output> -r <reference> -m 1

Run standard evolutionary analysis programs (run with -h for help text first):

# Run BEAST:

    piranha -f BEASTRunner

# Run ∂a∂i:

    piranha -f dadiRunner
    piranha -f dadiUncertainty

# Run RAxML:

    piranha -f MAGNET
    piranha -f RAxMLRunner

# Run RogueNaRok: 

    piranha -f RogueNaRokRunner

# Run SNAPP:

    piranha -f SNAPPRunner

Conduct post-processing of results from standard evolutionary analysis programs (run with -h for help text first):

# Process output from BEAST:

    piranha -f MLEResultsProc
    piranha -f BEASTPostProc

# Process output from ExaBayes:

    piranha -f ExaBayesPostProc

# Process output from MrBayes:

    piranha -f MrBayesPostProc

Use the documentation links in the sidebar at right to navigate this documentation and learn more about PIrANHA, and contact the author for technical support or raise an issue.

PIrANHA Publications

We are working on a paper describing PIrANHA while we develop towards major release v1.0 (hopefully later this year, in 2020). However, the alpha pre-release versions of PIrANHA have been used in several of our publications, including:

  • Bagley, J.C., Hickerson, M.J. and Johnson, J.B., 2018. Testing hypotheses of diversification in Panamanian frogs and freshwater fishes using hierarchical approximate Bayesian computation with model averaging. Diversity, 10(4), 120.
  • Bagley, J.C., Mayden, R.L. and Harris, P.M., 2018. Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils. PeerJ, 6, p.e5168.
  • Bagley, J.C., Uribe-Convers, S., Carlsen, M., Muchhala, N., 2020. Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study. Molecular Phylogenetics and Evolution. Available online. PubMed: https://www.ncbi.nlm.nih.gov/pubmed/32081762. doi: https://doi:10.1016/j.ympev.2020.106769.

Contact Info

Questions? Comments? Concerns? Bug fix requests? Feature requests for existing functions, or requests for new functions? If so, please get in touch here.

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

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 v0.4a4. 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.

Uninstall

Uninstalling Homebrew piranha

# Uninstall:
brew uninstall piranha && brew untap justincbagley/homebrew-tap ;
if [[ -f /usr/local/bin/local_piranha ]]; then rm -rf /usr/local/bin/local_piranha ; fi
if [[ -f /usr/local/bin/brew_piranha ]]; then rm -rf /usr/local/bin/brew_piranha ; fi

December 18, 2020 - Justin C. Bagley, Jacksonville, AL, USA

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