Updates makefile for release

Fixes compile issues Windows

Merge remote-tracking branch 'origin/master'

Fixes typo in sff.info

Adds fileExists function

Fixes opti phylip option

Fixes bug with shortcut files and windows parallelization

Merge pull request mothur#264 from mothur/1.39.0

1.39.0

Adjusts cutoff for agc and dgc methods

cluster and cluster.split

mothur#254

Fixes while building Windows