Hello, I need to align 2 sequences in hundreds of files and then write a list with the count of the mismatches in each file.
I thought I could use muscle for the alignments as it can run in command line and write a script to run all my files but then how do I count the mismatches of each alignment?
since they are just two protein sequences in each file I cannot use bowtie or similar. I also thought that maybe there is a way to convert a phylip or clustal format into sam so I can use some snp calling tools.
Does any one know how can I align and count the mismatches of all my files?
I thought I could use muscle for the alignments as it can run in command line and write a script to run all my files but then how do I count the mismatches of each alignment?
since they are just two protein sequences in each file I cannot use bowtie or similar. I also thought that maybe there is a way to convert a phylip or clustal format into sam so I can use some snp calling tools.
Does any one know how can I align and count the mismatches of all my files?
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