CONFIG

bedtools=/share/apps/genomics/bedtools2/bin/bedtools
mafft=/home/derstudent/software/mafft-7.310-with-extensions/bin/mafft
samtools=/share/apps/genomics/samtools-1.3/samtools
fasttree=/home/derstudent/software/FastTree/FastTree
trimal=/home/derstudent/software/trimAl/source/trimal
jmodeltest2=/home/derstudent/software/jmodeltest2-2.1.9r20160115/dist/jModelTest.jar
genometools=/share/apps/genomics/genometools-1.5.9/bin/gt#gt
hmmer=/share/apps/genomics/hmmer-3.1b2-linux-intel-x86_64/binaries/
blast=/share/apps/genomics/ncbi-blast-2.2.31+/bin/
mcl=/home/derstudent/software/mcl-14-137/bin/
geneconv=/home/joshd/software/GENECONV/geneconv
paup=/home/derstudent/software/PAUP4/paup
phylip=/home/derstudent/software/phylip-3.697/bin/
rscript=/home/derstudent/software/R/Rscript
perl=/home/derstudent/perl5/perlbrew/perls/perl-5.24.1/bin/perl
circos=/home/derstudent/software/circos/circos-0.69-6/bin/circos
pathd8=/home/derstudent/software/PATHd8/PATHd8
getorf=/home/derstudent/software/EMBOSS-6.6.0/bin/getorf