Question

remove gapped bases in MSA

1

Entering edit mode

7.2 years ago

Zev.Kronenberg 12k

I have a multiple sequence alignment represented as a "mulit-fasta." I want to remove any column that contains a gap.

Thought I would ask before writing my own.

msa alignment • 2.0k views

ADD COMMENT • link updated 7.2 years ago by abascalfederico ★ 1.2k • written 7.2 years ago by Zev.Kronenberg 12k

score 3 · Accepted Answer · 2017-01-24

3

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7.2 years ago

abascalfederico ★ 1.2k

Trimal is very versatile. Try with "-gt 0.0" http://trimal.cgenomics.org

ADD COMMENT • link 7.2 years ago by abascalfederico ★ 1.2k

2

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" -nogaps " is the flag. thanks.

ADD REPLY • link 7.2 years ago by Zev.Kronenberg 12k

0

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very helpful! Thanks!

trimal -in test -out test_nogaps_trimal -nogaps

ADD REPLY • link 6.2 years ago by Prakki Rama ★ 2.7k