How to read a multiple sequence alignment file?

Question

[sharmatina189059]

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.

[Joe]

You could take a look at alistat which 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

Answer 1

[manishaB]

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!