Merge 8ab243e0847d41cb34de04006bc53b2436f662b9 into 303ff51135c1ca79ab104358bde694d2cbd51fb1
Merge 2eecab4ccd1a41b67f853949aace546af62ef5e7 into 82df9ec6e30388ad40832e6045cac7dbf93fe84b
Merge pull request #5 from crosenth/master

Assuming function name was desired here
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
Merge e5957907aff994dbbe38f54262f79586a8c9fc12 into b8fe184cf60eb965ed3fdf2b7d26c0b541065af9
Add @nhoffman's fancy bootstrap script to README
Check for cmalign 1.1
Merge branch '04-infernal1.1'
Check for rppr before rerooting
Merge branches '04-infernal1.1' and 'master', commits 'refs/pull/1/head', 'refs/pull/1/merge', 'refs/pull/3/head', 'refs/pull/3/merge', 'refs/pull/5/head', 'refs/pull/7/head' and 'refs/pull/7/merge' of ssh://github.com/fhcrc/deenurp