How to create *.dist file?
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5.3 years ago
Arindam Ghosh ▴ 400

I need .dist file for MOTHUR. Using dist.seq gives error as "sequences are of dissimilar lengths*". Any alternate methods?

sequence mothur distance matrix phylogenetics • 1.3k views
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3.9 years ago

This method will calculate the distance matrix without considering Terminal Gap Penalty

dist.seqs(fasta=input.fasta, countends=F)

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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