{
HMMBuildThread hmmbuild = new HMMBuildThread(alignment);
hmmbuild.hmmbuildWaitTillComplete();
- SequenceI hmmSeq = alignment.getSequenceAt(1);
+ SequenceI hmmSeq = alignment.getSequenceAt(0);
HiddenMarkovModel hmm;
if (hmmSeq.isHMMConsensusSequence() && hmmSeq.getHMM() != null)
{