Does Bio::SearchIO parse the HTML output that BLAST creates using the -T option?
Yes, with a twist. You can modify Bio::SearchIO’s _readline() method such that it reads in the HTML and strips it of tags using the HTML::Strip module. Please note: We do not suggest parsing BLAST HTML output if it can be avoided. We actively support XML, tabular, and text output parsing of NCBI BLAST reports only; we have never supported parsing of NCBI BLAST HTML output directly through BioPerl and will not attempt to rectify problems where HTML output parsing post-stripping of the tags breaks but parsing text output works. Consider this fair warning.
