Question: How to create *.dist file?
0
gravatar for Arindam Ghosh
4.3 years ago by
Arindam Ghosh310
India
Arindam Ghosh310 wrote:

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

ADD COMMENTlink modified 3.0 years ago by Simply Bioinformatics170 • written 4.3 years ago by Arindam Ghosh310
0
gravatar for Simply Bioinformatics
3.0 years ago by
WashingtonDC
Simply Bioinformatics170 wrote:

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)

ADD COMMENTlink written 3.0 years ago by Simply Bioinformatics170
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1767 users visited in the last hour