Geneious Prime
Geneious Biologics
SeqPartitioner
Partition allele multisets from multiple alignments
Requires Geneious 6.1+
Open Source
Experimental
SeqPartitioner is a Geneious plugin for partitioning allele multisets. The plugin operates on alignments to produce various tables expressing the grouping of equivalent aligned nucleotide sequences and the number of differences between strains in terms of non-equivalent alleles.
Install the plugin by downloading the gplugin file and dragging it in to Geneious.
Once installed, run the plugin by selecting a multiple sequence alignment and selecting Partition Allele Multiset from the Tools menu.