Function reference

All functions

BatchRun()

Runs the whole analysis

ConcatenateAll()

Concatenate the sequences

CreateDir()

Create directory if needed

CreatePartitionFile()

Create partition file for raxml

FixNames()

Corrects taxon names

KeepClusters()

Find clusters to keep

ProcessSequencesByGeneConcat()

Process the output of phylotaR

ProcessSequencesByGeneSingle()

Process the output of phylotaR by gene

RemoveGappy()

Remove gappy columns

RunPhylotaR()

Runs phylotaR

RunRaxml()

Run raxml

SaveGenes()

Save genes to a file

TargetFactory()

Create the target workflow