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Pairwise.seqs (version 1.39.5.0)

fasta - Fasta:

align - Select a pairwise alignment method:

calc - Calc Method - Gap Penality:

countends - Countends:

Penalize terminal gaps

cutoff - Distance Cutoff threshold - ignored if not > 0:

Do not save any distances larger than this, a common value would be 0.10

Scoring match, mismatch, gapopen, and gapextend:

output - Distance Matrix Output Format:

Output logfile?:

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The pairwise.seqs command will calculate uncorrected pairwise distances between sequencesi as a column-formatted_distance_matrix or phylip-formatted_distance_matrix.