Man pages for fmichonneau/chopper
Alignment Manipulations and Data Preparation for Phylogenetic Analyses

alg2csvalgToCsv (alignemnt to CSV)
alg2nexConverts from PHYLIP or FASTA format to NEXUS format.
checkAmbiguityCheck for ambiguities in a DNA sequence
checkInternalGapsCheck for internal gaps in a DNA sequence.
chopperSequence data manipulation to ease phylogenetic analyses
completeSeqWithGapsComplete sequences with gaps.
concatenateAlignmentsConcatenate alignments
convertGapsConvert gap characters
convertRAxMLedgeLabelsConvert RAxML edge labels bootstrap values to node labels
cutAlignmentCut an alignment into individual partitions.
dealignDealign an alignment
fas2phyConverts FASTA files into PHYLIP format
mergeAlignmentMerge alignment files.
mergeSeqMerge sequences
nbaseNumber of bases
nexusPartitionCreateCreate a NEXUS-formatted partition file
raxmlPartitionCreateCreate a RAxML-formatted partition file
raxmlPartitionInfoInformation from a RAxML partition file
removeEmptySeqsRemove empty sequences
removeFastaCommentsRemove comments from FASTA files
splitAlignmentSplit alignments.
splitMultiAlignmentssplitMultiAlignments - split multiple alignments into...
fmichonneau/chopper documentation built on May 16, 2019, 1:43 p.m.