## Metagenomics / Filter sequence alignment with Mothur

### Description

Filters out columns from a fasta formatted sequence alignment.

### Parameters

None

### Details

Removes columns where every character is '-'. These empty 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. Removes also columns where one or more sequences have '.'

This tool is based on the Filter.seqs command of the Mothur package.

### Output

The analysis output consists of the following:

- filtered-aligned.fasta: Filtered alignment
- filtered-summary.tsv: Summary statistics for the filtered alignment
- filtered-log.txt: Lists the number of columns removed

### References

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.