Add partial support for nhmmer (version 3.1)
Add strand() so nhmmer can get strand data
Back this out, related tests are failing
Corrected, all SearchIO tests pass
Remove unused
Minor regex change
Sorry about this, analyzing new output files is leading to minor changes in regex's
Fix bug with score parsing in SearchIO::Exonerate

Exonerate can return negative scores, such as:
vulgar: aly-miR169a 0 21 + contig15750__54-177 19 40 + -3 M 21 21

These were not parsed correctly, resulting in an empty hit.

Edit the corresponding regular expression to account for a
possible minus symbol '-' before the digits.
Add unit test for SearchIO::Exonerate negative score case

Exonerate can return negative scores.
We need to have a unit test case for that.

- Add example output file with a negative score

- Add test case, which parses the example output file and looks for
  the score of the first hit of the first result.
  Test succeeds if the value found matches the expected one.
  If the negative score is not parsed (as before the bugfix), the
  test is not run, meaning a failure per the test plan.

The handling of failure could be improved to have a more meaningful
error than the catch-all "Bad plan".
Fixed some "undefined value" warnings when taxonomy file has empty lines

Added an empty last line in test files to be able to test for proper behavior
Fix warning, 'inclusion threshold'
FastAlign.pl

I did a bioperl script which uses the heuristic method of tfasty.
The query string is in amino acids and the hit string is in nucleotides.
There are extra nucleotides at the end of the hit string (option -diff and by
default = 10), that allow to verify if the intron start with common rules
(5'-GTGCGA-... for group II intron and after an exonic T for group I intron).

I'm glad to help the bioperl community!
Added script for breaking sequence files into equal sized parts.
Added script to cut subsequences out of a set of sequence files.