This tool was based on an early version of the Freebayes Galaxy wrapper that was included with Galaxy.  Since then, the included tool written by Daniel Blankenberg has been updated and is generally preferred since it works with newer versions of Freebayes and supports more options.

This tool uses Freebayes to call SNPS given a reference sequence and a BAM alignment file.
http://bioinformatics.bc.edu/marthlab/FreeBayes

Base alignment quality (BAQ) adjustment is a quality smoothing filter which applies a hidden 
markov model of read genesis to each alignment independently.  This is currently implemented
by samtools fillmd.  (See Biological Sequence Analysis Probabilistic Models of Proteins and 
Nucleic Acids by Durbin et. al. for more details.)


Updated in 2011 by Lance Parsons <lparsons@princeton.edu>, Lewis-Sigler Institute for Integrative Genomics, Princeton University