Man pages for fmichonneau/chopper
Alignment Manipulations and Data Preparation for Phylogenetic Analyses
| alg2csv | algToCsv (alignemnt to CSV) |
| alg2nex | Converts from PHYLIP or FASTA format to NEXUS format. |
| barMonophyletic | barMonophyletic |
| checkAmbiguity | Check for ambiguities in a DNA sequence |
| checkInternalGaps | Check for internal gaps in a DNA sequence. |
| chopper | Sequence data manipulation to ease phylogenetic analyses |
| cleanSeqLabels | cleanSeqLabels |
| completeSeqWithGaps | Complete sequences with gaps. |
| concatenateAlignments | Concatenate alignments |
| convertGaps | Convert gap characters |
| convertRAxMLedgeLabels | Convert RAxML edge labels bootstrap values to node labels |
| cutAlignment | Cut an alignment into individual partitions. |
| dealign | Dealign an alignment |
| expandPartitionInfo | expandPartitionInfo |
| fas2phy | Converts FASTA files into PHYLIP format |
| mergeAlignment | Merge alignment files. |
| mergeSeq | Merge sequences |
| nbase | Number of bases |
| nexusPartitionCreate | Create a NEXUS-formatted partition file |
| raxmlPartitionCreate | Create a RAxML-formatted partition file |
| raxmlPartitionInfo | Information from a RAxML partition file |
| removeEmptySeqs | Remove empty sequences |
| removeFastaComments | Remove comments from FASTA files |
| splitAlignment | Split alignments. |
| splitMultiAlignments | splitMultiAlignments - split multiple alignments into... |
