I have multiple sequence alignment files in the *maf format,
containing whole genome alignments from 6 species. I'm interested in
extracting the sequence surrounding the exons of ~16,000 genes. I was
wondering if it would be possible to run the Alignment Extractors tool
in batch? Would it be possible for me to run it on the command line?
Thanks ins Advance
By the way I'm a PhD student at Uppsala University, so any executables
that you provide will be used for academic purposes only.