Row order from multiple sequence alignment

Spencer Bliven <[email protected]> Mon, 29 Feb 2016 18:15:20 +0100

Newsgroups	gmane.comp.java.bio.general
Message-ID	<CA+P6ar=vGbe73ENUSAcwqGbsXWCSE42KD9mzr24F=ivaJzJ2gw@mail.gmail.com>

I'm creating a multiple sequence alignment using
Alignments.getMultipleSequenceAlignment, as described in the cookbook
<http://biojava.org/wiki/BioJava:CookBook3:MSA>. The problem is that the
returned profile has rows in a different order than the input array of
sequenced. How can I map from an index in the inputs to the rows of the
profile?

Thanks,
Spencer

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