phyloutils: A set of subcommands for phylogenetic computation.
PhyloUtils is a package shipped with a subset of scripts I used quite often
for phylogenetic computation. Currently included subcommands/scripts are
getGenomesFromGenbank, mergeGenbankGenomes, mergeMultipleFastaRecords,
generateShortNameTable, extractGenbankGenomicFna, extractGenbankProteins,
renameFastaFile, AMPHORE2HmmMarkerScanner, mergeEachMarkerProteinSet,
concatMarkersforEachGenome, convertMSFtoPhylip, runMSAonMarkers,
rnammerMarkerScanner, runSSUAlignAndMask, mergerRNASet,
runPartitionFinderProtein, runRAxML, replaceNameInTree,
runProdigal, runProkka, runHmmsearch.
This package is still under active development, use at your own risk.