Merge pull request #2 from reedacartwright/master

Merge latest changes
added .travis.yml
updated .travis.yml
cleanup
fix bug in indel_mrate handling
cleanup
added test cases and basic test
updated change-me, version
run test in  Travis CI
update path for test.
add travis badge.
Rename README to README.md
update README
update README.md
update CMakeLists to reflect new readme
Cleaned up after merging rebasing
Merge pull request #1 from denovogear/master

Merge Upstream