BARCOD encodes a multiple alignment according to the method developed by Véronique Barriel (C.R.Acad.Sci.III 317(7):693-701).
From a an existing alignment (which will not be changed) BARCOD builds a character matrix suitable for use in phylogeny recontstruction programs. The method allows to encode each insertion/deletion event as one single event (whatever the number of nucleotides involved), while retaining any indel common to two or more taxa as a possibly shared character.
The input file is a multiple alignment in Phylip, MASE or FASTA format. The output file is a character matrix in NEXUS format (Maddison et al., 1997).
BARCOD can work in two modes :