I manipulate a lot of huge alignments from PFAM in the rich, but extremely heavy, stockholm format. Sreformat was my command line tool of choice to convert from .sto to other formats (usually the one sequence per line .pfam format, but fasta would be ok), but I just found out it is not included anymore in the hmmer distribution at EBI. The older page at http://www.csb.yale.edu/userguides/seq/hmmer/docs/node3.html points to a broken link. Any idea where can I get sreformat, or a good command line equivalent that would be ok with dealing with alignments with hundreds of thousands of sequences?
The HMMER User's guide (http://www.csb.yale.edu/userguides/seq/hmmer/docs/main-expanded.html) provides an e-mail address for the person responsible. If the address is still valid, this would be the person to contact.
XSTK works pretty well:
http://www.phyloware.com/Phyloware/XSTK.html
You can use biopython to convert between formats. It has a good cookbook for basic analyses like this.
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