Hi,

I am using progressiveCactus https://github.com/glennhickey/progressiveCactus and I want to view the alignments and extract a consensus sequence. I don't want to use the UCSC genome browser. Does anyone know how to convert from hal or maf format (the only two that can be output or converted by this software) to something more universally readable? e.g. by Geneious. Alternatively a way to get the consensus from the alignment would be useful. Biopython does not seem to do it yet. I have read that BioRuby does, but I don't want to have to learn a whole new programming language just to do one conversion.

Thanks