Versioning added
Fixes for bug 3381

Additionally, clarified Hyphy.t to give better feedback.
Revert "Fixes for bug 3381"

This reverts commit 512380541696ffd931502a993101b98e0a7ac5af.
Fixes for bug 3381.
Better, cleaner warnings in tests.
Merge pull request #6 from daisieh/bug_3380

Fixes for bug 3380
Merge pull request #8 from daisieh/bug_3381_2

Bug 3381, again
Added version checking of Hyphy, updated create_wrapper based on version
merging adding_batchfile
Merge pull request #10 from bioperl/daisieh-adding_batchfile

merging adding_batchfile
deleted extra log files
Fixed synopsis
Consistent indentation
POD updates and insignificant code changes
Test refresh
More POD updates
POD update
Merge branch 'master' of github.com:bioperl/bioperl-run