[Biojava-l] Row order from multiple sequence alignment

[Spencer Bliven]

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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