update alignment model
- add top-level run script for tests
- save test output in output directories (to more easily ignore them)
requires infernal 1.1
- increment version to 0.0.2-dev
- add CHANGES.txt
- add bin/bootstrap.py (installs all dependencies in a virtualenv)
- update url for tax2tree
remove debugging code
drop MPI support
cmalign defaults to one cpu
define default number of cpus for cmalign using wrap.DEFAULT_CMALIGN_THREADS
Add @nhoffman's fancy bootstrap script to README
Check for cmalign 1.1
Merge branch '04-infernal1.1'