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Small programs to to usefuile tasks for phylogenetic analysis

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PhyloWidgits

Haskell code to perform small, useful tasks.

csv2Fasta converts csv files containig IPA languistic data to fasta/c files for analysis with PhyG (https://github.com/AMNH/PhyG).

csv2TCM Converts csv sound file to tcm for fastc language file

meanWords Calculates mean words of languages from fastc files (latex IPA representations)

ipaConvert Inter-converts ipa alphabet symbols to be parsable by phyloAlgoInfo (https://github.com/wardwheeler/PhyloAlgInfo)

getElements Returns file of alphabet symbols from fasta/c file

ia2Fasta Converts Implied Alignment output from PhyG and creates single fasta file by concatenating sequences with same taxon name, adding (or not) '#' between fragments

pruneRandGraph Prunes graph edges and vertices with 'rand' data key (or other)

randomSequences Naive random sequences generator based on to alphabet, average and variation length, and missing fraction

shuffleSequences Creates randomized sequences by shuffling elements of existing sequences, preserving distributional biases present in source data

Compilation

All are verified to compile with ghc-9.10.1 and cabal v 3.12.1

To install tools:

which ghcup || curl --proto '=https' --tlsv1.2 -sSf https://get-ghcup.haskell.org | sh which ghc || ghcup install ghc latest which cabal || ghcup install cabal latest cabal update

For each binary compilation :

cabal build binaryName --with-compiler ghc-9.10.1

References Wheeler, W. C. and P. M. Whiteley. 2015. Historical Linguistics as a Sequence Optimization Problem: Uto-Aztecan Language Evolution and Biogeography. Cladistics 31:113-125.

Wheeler, W. C., and A. Washburn. 2019. FASTC: A file format for multi-character sequence data. Cladistics, 35:573-575.

Wheeler, W. C., A. Washburn, and L. M. Crowley. 2024. PhylogeneticGraph (PhyG): A new phylogenetic search and optimization program. Cladistics, 40:97-105. https://github.com/AMNH/PhyG

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Small programs to to usefuile tasks for phylogenetic analysis

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