POY is a phylogenetic analysis software that supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc).
The multiple alignment procedures implemented in MALIGN are close parallels to those used to search for minimum length cladograms. The logic and software commands will be clear to those familiar with programs such as Hennig86, NONA, and PAUP.
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