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Screen.seqs (version 1.39.5.1)

fasta - Fasta to screen:

start - Remove sequences that start after position (ignored when negative):

end - Remove sequences that end before position (ignored when negative):

minlength - Remove sequences shorter than (ignored when negative):

maxlength - Remove sequences longer than (ignored when negative):

maxambig - Remove sequences with ambiguous bases greater than (ignored when negative):

maxhomop - Remove sequences with homopolymers greater than (ignored when negative):

criteria - Percent of sequences that an optimize value must match to be retained (ignored when negative):

optimize - Optimize selected paramenters:

qfile - Sequence Quality file to screen:

name - Sequence Names to screen:

group - Groups to screen:

summary file - as created by summary.seqs:

saves processing time when screening with parameters in the summary file

taxonomy - Taxonomy to screen:

count - a count_table:

generated by count.seqs

Perform screening using an alignment report?:

An alignment report is created by the align.seqs tool. If you provide the alignment report file you can screen your sequences using the following parameters: minsim, minscore, and maxinsert

Perform screening using a contigsreport?:

A contigsreport is created by the make.contigs tool. If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches

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 screen.seqs command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name, group, or align.report file.