Dataset,Program,Verbatim_command,Action,Best_time_in_seconds,Notes
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -i *fasta -f fasta -d dna -c,concatenation (fasta),21.6,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -f fasta -d dna -i *fasta -v -u phylip,fasta to phylip – converting 8295 single-gene files,16.03,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -f fasta -d dna -i *fasta -v -u nexus,fasta to nexus – converting 8295 single-gene files,15.92,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -f phylip -d dna -i *out.phy -v -u fasta,phylip to fasta – converting 8295 single-gene files,19.53,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -f phylip -d dna -i *out.phy -v -u nexus,phylip to nexus – converting 8295 single-gene files,16.52,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -f nexus-int -d dna -i *int-nex -v -u fasta,nexus int to fasta – converting 8295 single-gene files,29.68,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -f nexus-int -d dna -i *int-nex -v -u phylip-int,nexus int to phylip int – converting 8295 single-gene files,30.22,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -i *phy -f phylip -d dna -c -p part-jarvis-exons-phy -t conc-jarvis-exons-phy,concatenation (phylip sequential to fasta),22.47,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -i *nex -f nexus -d dna -c -p part-jarvis-exons-nex -t conc-jarvis-exons-nex,concatenation (nexus sequential to fasta),28.22,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -f fasta -d dna  -i conc-jarvis-exons-nex -l part-jarvis-exons-nex -u fasta,splitting by partition (fasta to fasta),23.9,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -i *-out.nex -f nexus -d dna -c -p part-jarvis-exons-nex.nexus -t conc-jarvis-exons-nex.nexus -u nexus,concatenation (nexus sequential to nexus sequential),26.69,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,AMAS,time -p AMAS.py -i $FILE -d aa -f fasta -s -o summ-$FILE,summary-concatenated alignment (fasta),481.9,
Jarvis_et_al2014_uce_w_gator UCE individual alignments without outgroups,AMAS,time -p AMAS.py -i *fasta -f fasta -d dna -c,concatenation (fasta),13.76,
Jarvis_et_al2014_uce_w_gator UCE individual alignments without outgroups,AMAS,time -p AMAS.py -i *fasta -f fasta -d dna -c -e,concatenation (fasta),19.22,
Jarvis_et_al2014_uce_w_gator UCE individual alignments without outgroups,AMAS,time -p AMAS.py -i *fasta -d dna -f fasta -c -t conc-jarvis-uces-fas,concatenation (fasta),19.22,
Jarvis_et_al2014_uce_w_gator UCE individual alignments without outgroups,AMAS,time -p AMAS.py -i $FILE -d aa -f fasta -s -o summ-$FILE,summary-concatenated alignment (fasta),308.96,
Johnson_et_al_2013-5214genes,AMAS,time -p AMAS.py -i matrix*-out.fas -d aa -f fasta -c -t conc-johnson5214-aa-fas,concatenation (fasta),2.0,
Johnson_et_al_2013-5214genes,AMAS,time -p AMAS.py -f phylip-int -d aa  -i matrix-5214genes.phy -l matrix-5214genes_partitions.txt -u fasta,splitting by partition (phylip-int to fasta),4.574,
Johnson_et_al_2013-5214genes,AMAS,time -p AMAS.py -f fasta -d aa -i matrix-5214genes*fas -s,summary-single locus (summaries on concatenated file take the approximately the same time),29.39,
Johnson_et_al_2013-5214genes,AMAS,time -p AMAS.py -f fasta -d aa  -i conc-johnson5214-aa-fas -l partitions.txt -u fasta,splitting by partition (fasta to fasta),1.75,
Johnson_et_al_2013-5214genes,AMAS,time -p AMAS.py -f fasta -d aa -i 5214concat.fas -v -u phylip,fasta to phylip – converting concatenated alignment,1.123,
Johnson_et_al_2013-5214genes,AMAS,time -p AMAS.py -f fasta -d aa -i 5214concat.fas -v -u nexus,fasta to nexus – converting concatenated alignment,1.154,
Johnson_et_al_2013-5214genes,AMAS,time -p AMAS.py -f fasta -d aa -i 5214concat.fas -v -u nexus,fasta to nexus sequential – converting concatenated alignment,1.06,
Johnson_et_al_2013-5214genes,AMAS,time -p AMAS.py -f fasta -d aa -i 5214concat.fas -v -u nexus-int,fasta to nexus interleaved – converting concatenated alignment,378.02,command ran only once
Johnson_et_al_2013-5214genes,AMAS,time -p AMAS.py -f fasta -d aa -i 5214concat.fas -v -u phylip,fasta to phylip – converting concatenated alignment,1.06,
Johnson_et_al_2013-5214genes,AMAS,time -p AMAS.py -f fasta -d aa -i 5214concat.fas -v -u phylip-int,fasta to phylip interleaved – converting concatenated alignment,374.56,command ran only once
Johnson_et_al_2013-5214genes,AMAS,time -p AMAS.py -i $FILE -d dna -f fasta -s -o summ-$FILE,summary-concatenated alignment (fasta),29.6,
Misof_et_al_2014-aa_alignments,AMAS,time -p AMAS.py -i *fas -f fasta -d aa -c,concatenation (fasta),4.56,
Misof_et_al_2014-aa_alignments,AMAS,time -p AMAS.py -i *fas -f fasta -d aa -c -e,concatenation (fasta),33.86,
Misof_et_al_2014-aa_alignments,AMAS,time -p AMAS.py -i $FILE -d dna -f fasta -s -o summ-$FILE,summary-concatenated alignment (fasta),73.32,
Misof_et_al_2014-aa_alignments,FASconCAT-G,time -p perl FASconCAT-G_v1.02.pl -s,concatenation (fasta),1388.67,command ran only once
Johnson_et_al_2013-5214genes,FASconCAT-G,time -p perl FASconCAT-G_v1.02.pl -s,concatenation (fasta),516.86,
Johnson_et_al_2013-5214genes,FASconCAT-G-i,time -p perl FASconCAT-G_v1.02.pl -s -i,concatenation (fasta),73.23,
Misof_et_al_2014-aa_alignments,FASconCAT-G-i,time -p perl FASconCAT-G_v1.02.pl -s -i,concatenation (fasta),260.13,
Jarvis_et_al_2014-8295exons-dna (Amino acid alignments translated to DNA) with outgroups included,Phyutility,time -p java -jar phyutility.jar -concat -in *fasta -out phyut_jarvis-exons,concatenation (fasta),12236.53,command ran only once
Jarvis_et_al2014_uce_w_gator UCE individual alignments without outgroups,Phyutility,time -p java -jar phyutility.jar -concat -in *fasta -out phyut_jarvis-uces,concatenation (fasta),3655.36,command ran only once
Misof_et_al_2014-aa_alignments,Phyutility,time -p java -jar phyutility.jar -concat -in *fas -out phyut_misof-aa,concatenation (fasta),584.63,command ran only once
Johnson_et_al_2013-5214genes,Phyutility,time -p java -jar phyutility -concat -in matrix-5214*fas -out phyut_5214-test1,concatenation (fasta),619.79