recover GenericWebAgent from Bio-EUtilities
missing request for marker name in the call
doc: fix indentation, remove hard tabs and trailing whitespace
Bio::Cluster::SequenceFamily - bug fixes and performance

* fix bug when accessing the Bio::Species object. If a Bio::Seq object
  had no Bio::Species information, can('species') still returned true
  but the method would then return undef, and give an error next.
* when using multiple criteria, objects matching more than one criteria
  would appear repeated. Not anymore.
* if for some reason there's two equal objects on the family (same
  reference), they will also appear only once in the results.
* some improved performance is expected for large families when using
  multiple criteria now.
Add support for version 4, all tests pass
Merge branch 'master' of github.com:bioperl/bioperl-live

Add support for meme verions 4
Annotation: fix typo on test
remove hard tabs and trailing whitespace from some test files
tests for inheritance should belong on the child class, not the parent class
Add dna_to_aa_aln method and tests
Merge branch 'master' of github.com:bioperl/bioperl-live
maint: remove hard tabs and trailing whitespace
Bug 3415
tests: move tests from Root to Assembly and SeqIO (fixing commit 527d74f9e9d39fe3590a65a69fc1e8c24cb94540)
maint: remove files that have been moved to a separate Bio-Root distribution
maint: update Changes after removing files from Bio-Root
maint: remove files that have been moved to a separate Bio-Coordinate distribution
Initialize the Strand value if missing before performing a "flip_strand"
for an Atomic location, or it will silently fail
Split/flip_strand now makes a strand consistency check in all sublocations,
and sets Guide Strand accordingly. In case of mixed strands (trans-splicing),
it reverse the sublocations order to produce the correct revcom transcript
Split/guide_strand now makes a consistency check of the sublocations
strand values to set its own value, giving undef for mixed strands