cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf56.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf56.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf57.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf59.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf59.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf61.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf61.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf63.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf63.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf64.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf64.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf65.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf66.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf66.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf67.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf67.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf68.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf68.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf70.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf70.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf72.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf72.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf73.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf73.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf74.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf74.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf75.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf75.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf76.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf76.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf78.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf78.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf79.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf79.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf80.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf80.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf83.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf83.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s Ymf84.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf84.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s atp9.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-atp9.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s cob.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s cox1.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-cox1.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s cox2.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-cox2.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s heme.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-heme.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad10.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad10.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad1a.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad1a.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad1b.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad1b.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad2.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad2.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad2b.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad2b.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad3.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad3.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad4-2.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad4-2.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad4.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad4.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad4l.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad4l.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad5.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad5.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad6.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad6.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad7.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad7.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s nad9.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad9.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s rpl14.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-rpl14.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s rpl16.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-rpl16.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s rpl2.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-rpl2.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s rpl6.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-rpl6.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s rps12.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-rps12.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s rps13.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-rps13.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s rps14.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-rps14.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s rps19.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-rps19.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 cd /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix; module load raxml/8.0.26; raxml -f a -s rps3.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-rps3.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345