abyss: modernize autotools deps
adol-c: modernize autotools deps
beagle: modernize autotools deps
fastx_toolkit: modernize autotools deps
hmmer: modernize autotools deps
minc: modernize autotools deps
moab: modernize autotools deps
mrbayes: modernize autotools deps
openni: modernize autotools deps
sga: modernize autotools deps
snp_sites: modernize autotools deps
z3: modernize autotools deps