How to find out the mismatch position from MUSCLE or CLUSTALW output?

Question

[mbk0asis]

Hello, everyone!

I'm trying to find out the positions of SNP between human and orangutan mRNAs.

I ran MUSCLE mRNAs from the two species and obtained clustal-like output.

All I need is finding the position of SNP. I've been looking for tools for more than a week, but none of them seemed working in my case. Mostly because my lack of computer skills(?) like coding, compiling and so on.

If anyone knows such tools, please let me know!

Thank you

[SES]

Are you looking for an alignment viewer to visually find differences, or a command-line tool/script to print out indel positions?

[mbk0asis]

A command line tool that can print out snp positions would be great

Answer 1

[h.mon]

Have a look at SNP-sites.