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.
The dist.seqs command will calculate uncorrected pairwise distances between aligned sequences. The command will generate a column-formatted_distance_matrix that is compatible with the column option in the read.dist command. The command is also able to generate a phylip-formatted_distance_matrix. There are several options for how to handle gap comparisons and terminal gaps.
v.1.20.0: Updated to Mothur 1.33