Merge pull request #77 from jrrideout/master

Fix pynast 1.2.1 filename
Updates versions of NumPy and R
Merge pull request #78 from samfway/update_deps

Update versions of NumPy and R
added paired end assembler apps
Merge pull request #79 from gregcaporaso/paired-end-assemblers

added paired end assembler apps
Fix seqprep target