update pymol to 1.7
mitofy 20120322: New formula

Mitofy was developed to assist in the annotation of genes and tRNAs in
seed plant mitochondrial genomes.
Update ASL to 20140205.

Closes #659.
novoalign 3.02.02
gatk 2.8-1: New formula

The Genome Analysis Toolkit or GATK is a software package developed at
the Broad Institute to analyse next-generation resequencing data.
Revert "gatk 2.8-1: New formula"

This reverts commit e059df972fb156b1d59a0df9bd2d9a448ca831b8.
fasta 36.3.6d: update checksum

Closes #658
Remove deprecated patch.
beagle 2.1

Include persistent reference to release 2.1.

Closes #652
libsequence 1.8.0

updated libsequence 1.7.6 to 1.8.0, added HEAD

Closes #637
raxml 8.0.1

Closes #618
bali-phy 2.2.0

No longer depends on gsl.
Requires C++11.

Closes #609
infernal 1.1

Closes #595
clustal-omega 1.2.0

Closes #592
clustal-omega: Add a test
fastx_toolkit 0.0.14: Requires C++11

Closes #620
sfscode 20130725: New formula

Closes #543
stacks 1.09: Remove the patch

Closes #515
stacks 1.12

No longer fails to build with clang.
PEAR 0.9.0: New Formula

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger.

http://sco.h-its.org/exelixis/web/software/pear/

Closes #651