Dataset,Data_type,Program,Function,Verbatim_command,Avg_time
Johnson_et_al_2013,amino acid,AMAS,concatenation-fig,time -p amas concat -i ./Johnson_2013/matrix-5214genes*fas -f fasta -d aa,1.87
Misof_et_al_2014,amino acid,AMAS,concatenation,time -p amas concat -i ./Misof_2014/aa_alignments/OGs_fasta/*aa.fas -f fasta -d aa,4.05
Jarvis_et_al_2014-uces,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/uce-filtered-alignments-w-gator/*fasta -f fasta -d dna,10.91
Jarvis_et_al_2014-exons,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna,17.85
Johnson_et_al_2013,amino acid,AMAS,concatenation,time -p amas concat -i ./Johnson_2013/matrix-5214genes*fas -f fasta -d aa --cores 12,1.01
Misof_et_al_2014,amino acid,AMAS,concatenation,time -p amas concat -i ./Misof_2014/aa_alignments/OGs_fasta/*aa.fas -f fasta -d aa --cores 12,2.92
Jarvis_et_al_2014-uces,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/uce-filtered-alignments-w-gator/*fasta -f fasta -d dna --cores 12,5.48
Jarvis_et_al_2014-exons,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna --cores 12,8.09
Jarvis_et_al_2014-exons,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna -u nexus,15.04
Jarvis_et_al_2014-exons,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna -u phylip,15.07
Jarvis_et_al_2014-exons,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna -u phylip-int,15.91
Jarvis_et_al_2014-exons,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna -u nexus-int,15.98
Jarvis_et_al_2014-exons,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna -u nexus --cores 12,4.87
Jarvis_et_al_2014-exons,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna -u phylip --cores 12,4.84
Jarvis_et_al_2014-exons,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna -u phylip-int --cores 12,6.49
Jarvis_et_al_2014-exons,nucleotide,AMAS,concatenation,time -p amas concat -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna -u nexus-int --cores 12,6.14
Johnson_et_al_2013,amino acid,AMAS,summary,time -p amas summary -i ./Johnson_2013/matrix-5214genes*fas -f fasta -d aa,33.69
Misof_et_al_2014,amino acid,AMAS,summary,time -p amas summary -i ./Misof_2014/aa_alignments/OGs_fasta/*aa.fas -f fasta -d aa,78.58
Jarvis_et_al_2014-uces,nucleotide,AMAS,summary,time -p amas summary -i ./Jarvis_2014/uce-filtered-alignments-w-gator/*fasta -f fasta -d dna,346.26
Jarvis_et_al_2014-exons,nucleotide,AMAS,summary,time -p amas summary -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna,508.95
Johnson_et_al_2013,amino acid,AMAS,summary,time -p amas summary -i ./Johnson_2013/matrix-5214genes*fas -f fasta -d aa --cores 12,10.37
Misof_et_al_2014,amino acid,AMAS,summary,time -p amas summary -i ./Misof_2014/aa_alignments/OGs_fasta/*aa.fas -f fasta -d aa --cores 12,24.22
Jarvis_et_al_2014-uces,nucleotide,AMAS,summary,time -p amas summary -i ./Jarvis_2014/uce-filtered-alignments-w-gator/*fasta -f fasta -d dna --cores 12,70.13
Jarvis_et_al_2014-exons,nucleotide,AMAS,summary,time -p amas summary -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna --cores 6,112.41
Johnson_et_al_2013,amino acid,AMAS,summary-fig,time -p amas summary -i j2013.fasta -f fasta -d aa,34.5
Misof_et_al_2014,amino acid,AMAS,summary-fig,time -p amas summary -i m2014.fasta -f fasta -d aa,89.26
Jarvis_et_al_2014-uces,nucleotide,AMAS,summary-fig,time -p amas summary -i j2014-uces.fasta -f fasta -d dna,380.03
Jarvis_et_al_2014-exons,nucleotide,AMAS,summary-fig,time -p amas summary -i j2014-exon.fasta -f fasta -d dna,599.04
Johnson_et_al_2013,amino acid,AMAS,summary,time -p amas summary -i j2013.nexus -f nexus -d aa,35.28
Johnson_et_al_2013,amino acid,AMAS,summary,time -p amas summary -i j2013.phylip -f phylip -d aa,34.83
Johnson_et_al_2013,amino acid,AMAS,summary,time -p amas summary -i j2013.int-phy -f phylip-int -d aa,37.97
Johnson_et_al_2013,amino acid,AMAS,summary,time -p amas summary -i j2013.int-nex -f nexus-int -d aa,29.8
Jarvis_et_al_2014-exons,nucleotide,AMAS,replicate,time -p amas replicate -r 1000 100 -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna,96.73
Jarvis_et_al_2014-exons,nucleotide,AMAS,replicate,time -p amas replicate -r 1000 100 -i ./Jarvis_2014/pep2cds/OGs/*fasta -f fasta -d dna --cores 12,86.78
Johnson_et_al_2013,amino acid,AMAS,splitting,time -p amas split -i j2014-exon.fasta -f fasta -d aa -l j2014-exon-partitions.txt,17.52
Johnson_et_al_2013,amino acid,AMAS,splitting,time -p amas split -i j2014-exon.fasta -f fasta -d aa -l j2014-exon-partitions.txt --cores 12,20.17
Johnson_et_al_2013,amino acid,Phyutility,concatenation-fig,time -p java -jar ./phyutility/phyutility.jar -concat -in ./Johnson_2013/phyut/* -out phyut_j2013-test,643.95
Misof_et_al_2014,amino acid,Phyutility,concatenation,time -p java -jar ./phyutility/phyutility.jar -concat -in ./Misof_2014/aa_alignments/OGs_fasta/phyut/* -out phyut_misof-aa-test,577.71
Jarvis_et_al_2014-uces,amino acid,Phyutility,concatenation,time -p java -jar ./phyutility/phyutility.jar -concat -in ./Jarvis_2014/uce-filtered-alignments-w-gator/phyut/* -out phyut_jarvis-uces-test,3569.32
Jarvis_et_al_2014-exons,amino acid,Phyutility,concatenation,time -p java -jar ./phyutility/phyutility.jar -concat -in ./Jarvis_2014/pep2cds/OGs/phyut/* -out phyut_jarvis-exon-test,12209.58
Johnson_et_al_2013,amino acid,AMAS,conversion,time -p amas convert -i *z-out.nex -f nexus -d aa --out-format fasta,3.12
Johnson_et_al_2013,amino acid,AMAS,conversion,time -p amas convert -i *z-out.nex -f nexus -d aa --out-format phylip,2.85
Johnson_et_al_2013,amino acid,AMAS,conversion,time -p amas convert -i *z-out.nex -f nexus -d aa --out-format nexus-int,2.92
Johnson_et_al_2013,amino acid,AMAS,conversion,time -p amas convert -i *z-out.nex -f nexus -d aa --out-format phylip-int,3.16
Johnson_et_al_2013,amino acid,AMAS,conversion,time -p amas convert -i *z-out.nex -f nexus -d aa --out-format fasta --cores 12,1.87
Johnson_et_al_2013,amino acid,AMAS,conversion,time -p amas convert -i *z-out.nex -f nexus -d aa --out-format phylip --cores 12,1.37
Johnson_et_al_2013,amino acid,AMAS,conversion,time -p amas convert -i *z-out.nex -f nexus -d aa --out-format nexus-int --cores 12,1.64
Johnson_et_al_2013,amino acid,AMAS,conversion,time -p amas convert -i *z-out.nex -f nexus -d aa --out-format phylip-int --cores 12,1.45
Johnson_et_al_2013,amino acid,FASconCAT-G-w-summ,concatenation-fig,time -p perl /home/jlabadmin/MarekBorowiec/AMAS_benchmark/FASconCAT-G_v1.02.pl -s,493.3
Johnson_et_al_2013,amino acid,FASconCAT-G-no-summ,concatenation-fig,time -p perl /home/jlabadmin/MarekBorowiec/AMAS_benchmark/FASconCAT-G_v1.02.pl -s -i,36.23
Misof_et_al_2014,amino acid,FASconCAT-G-w-summ,concatenation,time -p perl /home/jlabadmin/MarekBorowiec/AMAS_benchmark/FASconCAT-G_v1.02.pl -s,1379.02
Misof_et_al_2014,amino acid,FASconCAT-G-no-summ,concatenation,time -p perl /home/jlabadmin/MarekBorowiec/AMAS_benchmark/FASconCAT-G_v1.02.pl -s -i,256.58