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Filter.seqs (version
Additional Alignment Files
Additional Alignment File 0
Ignore any column that only contains gap characters (i.e. '-' or '.')
Remove a column if the trump character is found at that position in any sequence of the alignment
Removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences
A file should only contain one line consisting of 0's and 1's

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 filter.seqs command removes columns from alignments based on a criteria defined by the user. For example, alignments generated against reference alignments (e.g. from RDP, SILVA, or greengenes) often have columns where every character is either a '.' or a '-'. These columns are not included in calculating distances because they have no information in them. By removing these columns, the calculation of a large number of distances is accelerated. Also, people also like to mask their sequences to remove variable regions using a soft or hard mask (e.g. Lane's mask). This type of masking is only encouraged for deep-level phylogenetic analysis, not fine level analysis such as that needed with calculating OTUs.

v.1.20.0: Updated to Mothur 1.33