Talk about strict vs relaxed PHYLIP; Fixed extra bracket
Adding _AurgumentList for passing in multiple filenames for the samtools wrapper

Explaination for trailing spaces in _ArgumentList documentation
Class docstring; fix typo; use comment not multiline string
Formatting changes
Adding wrapper for the samtools command line tool

Squashed commit of pull request #180
Thank Saket for the samtools wrapper
Install samtools under TravisCI (to test wrapper)
Windows case insensitive; Actually use the detected samtools binary
Windows case insensitive; Actually use the detected bwa binary
Removed print statements; Use assertEqual
Comment out unimplemented test functions

(Gave false impression of better coverage than actually have)
Install BWA under TravisCI to test the wrapper