cleaned up missing imports
cleaned up imports
removed unused function
modified imports
updated to use the new Alignment object - note that the tests did not change, so this is good confirmation that we're achieving the same functionality
removed function that is now no longer used. go scikit-bio
removed cogent dependencies from remove_outliers - note that no changes to the test data were made, only had to modify to use the skbio Alignment interface
decogented... fixes #1500
fixed typo
fixed doc error
doc fix
modified based on @ElBrogrammers comment
Merge pull request #1554 from gregcaporaso/issue-1500

removes dependencies on cogent from filter_alignment, which was a big hold-up