I need .dist file for MOTHUR. Using dist.seq gives error as "sequences are of dissimilar lengths*". Any alternate methods?
This method will calculate the distance matrix without considering Terminal Gap Penalty
Alternative method is To trim your fasta reads to the most common length
1) trim.seqs(fasta=input.fasta, minlength=300, maxlength=300)
2) dist.seqs(fasta=input.trim.fasta, countends=T)
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