###############################
## START PoSeiDon: 1488360010
###############################

PROJECT_DIR=/your/project/dir

#CALCULATIONS ON FULL ALIGNMENT...

#BUILD ALIGNMENT...
translatorx.pl -i $PROJECT_DIR/bats_mx1.fna -p M -o $PROJECT_DIR/aln/bats_mx1

#BUILD PHYLOGENY...
raxmlHPC-PTHREADS-SSE3 -T 45 -f a -# 100 -x 1234 -p 1234 -s $PROJECT_DIR/aln/bats_mx1.nt_ali.nogaps.fasta -n nt -m GTRGAMMA -N 1000 -w $PROJECT_DIR/phylo/

nw_display -v 50 -i 'font-size:11' -l 'font-size:16;font-family:helvetica;font-style:italic' -d 'stroke:black;fill:none;stroke-width:2;stroke-linecap:round' -Il -w 650 -b 'opacity:0' -s $PROJECT_DIR/phylo/RAxML_bipartitionsBranchLabels.nt.corrected > $PROJECT_DIR/phylo/RAxML_bipartitionsBranchLabels.nt.scale.svg

nw_reroot $PROJECT_DIR/phylo/RAxML_bipartitionsBranchLabels.nt.corrected  > $PROJECT_DIR/phylo/RAxML_bipartitionsBranchLabels.nt.corrected.rooted

raxmlHPC-PTHREADS-SSE3 -T 45 -f a -# 100 -x 1234 -p 1234 -s $PROJECT_DIR/aln/bats_mx1.nt_ali.nogaps.fasta -n aa -m PROTGAMMAWAG -N 1000 -w $PROJECT_DIR/phylo/

nw_display -v 50 -i 'font-size:11' -l 'font-size:16;font-family:helvetica;font-style:italic' -d 'stroke:black;fill:none;stroke-width:2;stroke-linecap:round' -Il -w 650 -b 'opacity:0' -s $PROJECT_DIR/phylo/RAxML_bipartitionsBranchLabels.aa.corrected > $PROJECT_DIR/phylo/RAxML_bipartitionsBranchLabels.aa.scale.svg

nw_reroot $PROJECT_DIR/phylo/RAxML_bipartitionsBranchLabels.aa.corrected  > $PROJECT_DIR/phylo/RAxML_bipartitionsBranchLabels.aa.corrected.rooted

#RUN MODELSELECTION...
(echo "$PROJECT_DIR/aln/bats_mx1.nt_ali.nogaps.fasta"; echo "$PROJECT_DIR/phylo/RAxML_bipartitionsBranchLabels.nt.unshod.tree"; echo "4"; echo "1"; echo "0.05"; echo "$PROJECT_DIR/model_selection/bats_mx1.nt_ali.nogaps.fasta.result") | mpirun -np 45 HYPHYMPI ModelTest.bf

#RUN GARD...
(echo "$PROJECT_DIR/aln/bats_mx1.nt_ali.nogaps.fasta"; echo "$PROJECT_DIR/aln/bats_mx1.nt_ali.nogaps.fasta"; echo "010010"; echo "2"; echo "3"; echo "$PROJECT_DIR/gard/gard") | mpirun -np 45 HYPHYMPI GARD.bf

#GARDProcessor
(echo "$PROJECT_DIR/gard/gard_finalout"; echo "$PROJECT_DIR/gard/gard_splits") | mpirun -np 45 HYPHYMPI GARDProcessor.bf

#RUN CODEML ON FULL ALIGNMENT...
codeml $PROJECT_DIR/codeml/F61/M0/codeml.ctl
codeml $PROJECT_DIR/codeml/F61/M1a/codeml.ctl
codeml $PROJECT_DIR/codeml/F61/M2a/codeml.ctl
codeml $PROJECT_DIR/codeml/F61/M7/codeml.ctl
codeml $PROJECT_DIR/codeml/F61/M8/codeml.ctl
codeml $PROJECT_DIR/codeml/F61/M8a/codeml.ctl
codeml $PROJECT_DIR/codeml/F1X4/M0/codeml.ctl
codeml $PROJECT_DIR/codeml/F1X4/M1a/codeml.ctl
codeml $PROJECT_DIR/codeml/F1X4/M2a/codeml.ctl
codeml $PROJECT_DIR/codeml/F1X4/M7/codeml.ctl
codeml $PROJECT_DIR/codeml/F1X4/M8/codeml.ctl
codeml $PROJECT_DIR/codeml/F1X4/M8a/codeml.ctl
codeml $PROJECT_DIR/codeml/F3X4/M0/codeml.ctl
codeml $PROJECT_DIR/codeml/F3X4/M1a/codeml.ctl
codeml $PROJECT_DIR/codeml/F3X4/M2a/codeml.ctl
codeml $PROJECT_DIR/codeml/F3X4/M7/codeml.ctl
codeml $PROJECT_DIR/codeml/F3X4/M8/codeml.ctl
codeml $PROJECT_DIR/codeml/F3X4/M8a/codeml.ctl


#BREAKPOINTS DETECTED, ALIGNMENT ACCORDINGLY SPLITTED