How to read a multiple sequence alignment file?
Dear all
I have a example file like
>Sequence1
GARFIELDTHELASTFATCAT
>Sequence2
GARFIELDTHEFASTCAT
>Sequence3
GARFIELDTHEVERYFASTCAT
>Sequence4
THEFATCAT
>Sequence5
GARFIELDTHEVASTCAT
I need to do multiple sequence alignment and count number of variation. Is there any tool to count those variation. I am going to use clustalW for this purpose.
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sharmatina189059 •
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sharmatina189059 •
1 answer
GSAlign is a tool which outputs a .vcf (variant call format) file containing number of insertions, deletions or substitutions in query genome against the reference genome taken. You can check if the tool helps. https://github.com/hsinnan75/GSAlign
Good luck!
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manishaB •
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You could take a look at
alistatwhich will provide some simple descriptive numbers about a given alignment (after you've aligned it with clustal (or whatever).http://www.csb.yale.edu/userguides/seq/hmmer/docs/node27.html