[EMBOSS] File standards for reporting analysis tool results

[Clancy, Kevin]

Folks
I'm trying to identify if there are any well supported file formats that folk use for reporting results from analysis tools. So MSA or Nexus formats have been devised for multiple alignments and phylogenetics analyses. The work being done on SAM/BAM files standardizes reporting mapped next gen data, eg with CIGAR strings. There has been some use of GFF and BAM files for reporting parts of an analysis. I was wondering if there was a generalized format used by EMBOSS tools to standardize their outputs? Has anyone used BSML or other file formats standards in this fashion?

Thanks for your feedback.
kevin

Kevin Clancy, PhD
Invitrogen: Life tech
Carlsbad, CA 92008