How to create *.dist file?

Question

[Arindam Ghosh]

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

Answer 1

[Simply Bioinformatics]

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)