Sanger quicktree phylogenetic tree prog formula

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Update formulae for version 0.7

* Use new "url" features
* Use keg_only DSL
* Use "skip_clean :all" DSL
* Whitespace and style cleanups
* Make bash invocations less silly
* Use new man2-man8 helpers
* Remove "FileUtils." since it is included in Formula
* Use real names for deps instead of aliases
* ENV.x11 now updates path, so remove that from individual brews
added clustalW build (some people still use it!)

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
FSA: Fast Statistical Alignment

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Added EMBOSS Bioinformatics suite

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Added bowtie short read aligner

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Paml 4.4c

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Add bwa

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
bowtie 0.12.7

Updated and fixes #3043
Adding formula for Primer3, a bioinformatics tool.

Made changes that adamv suggested to the formula.

Closes #3771.

Signed-off-by: Mike McQuaid <mike@mikemcquaid.com>
Update clustal-w URL, fixes #4051
samtools 0.1.12a

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
samtools 0.1.13

OS X patch no longer needed, as issue was fixed upstream.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
tophat 1.2.0

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Use ruby style for inheritance.
added NCBI BLAST 2.2.24+

Closes #4033.

Signed-off-by: Mike McQuaid <mike@mikemcquaid.com>
blast: audit warning
samtools 0.1.14

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
muscle 3.8.31

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
samtools 0.1.15

Signed-off-by: Adam Vandenberg <flangy@gmail.com>