HyPhy_commands

##### RELAX #####
##tree: (Medex,(Bger,(Znev,(Csec,(Rflav,Mnat{F})))));  #for each species {F} was moved to the corresponding branch

name=$(head -n $SGE_TASK_ID filenames.txt | tail -n 1)  #filenames contains names of alignments

mkdir Out_${name}

cd Out_${name}

~/hyphy_2.5.5_NOAVX_installation/bin/hyphy relax CPU=5 --alignment ~/${name} --tree ~/relax.tree --rates 2 --test F

cd ../


##### aBSREL #####
name=$(head -n $SGE_TASK_ID filenames.txt | tail -n 1)

mkdir Out_${name}

cd Out_${name}

~/hyphy_2.5.5_NOAVX_installation/bin/hyphy absrel CPU=5 --alignment ~/${name} --tree ~/treefile --branches F > ${name}.out

cd ../