added tests for phylogeny.py and refactored the module to unify file system access.
Merge pull request #143 from LinguList/master

Not many modifications, but some cleanup of phylogeny.py, especially regarding documentation and print-statements
more tests and refactoring
Merge pull request #145 from xrotwang/phylogeny

Phylogeny
refactored sca to use shared utilities and be more testable
Merge pull request #146 from xrotwang/util

refactored sca to use shared utilities and be more testable
update sca, fix one bug in output and fixes #147