cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Alexandrium-monilatum-CCMP3105.MUSCLE.fa -n Alexandrium-monilatum-CCMP3105.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 &
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Alexandrium-temarense-CCMP1771.MUSCLE.fa -n Alexandrium-temarense-CCMP1771.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 &
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Amoebophrya-sp.-Ameob2.MUSCLE.fa -n Amoebophrya-sp.-Ameob2.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Amphidinium-carterae-CCMP1314.MUSCLE.fa -n Amphidinium-carterae-CCMP1314.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Azadinium-spinosum-3D9.MUSCLE.fa -n Azadinium-spinosum-3D9.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Brandtodinium-nutriculum-RCC3387.MUSCLE.fa -n Brandtodinium-nutriculum-RCC3387.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Ceratium-fusus-PA161109.MUSCLE.fa -n Ceratium-fusus-PA161109.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Chromera-velia-CCMP2878.MUSCLE.fa -n Chromera-velia-CCMP2878.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Crypthecodinium-cohnii-Seligo.MUSCLE.fa -n Crypthecodinium-cohnii-Seligo.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Dinophysis-acuminata-DAEP01.MUSCLE.fa -n Dinophysis-acuminata-DAEP01.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Durinskia-baltica-CSIRO_CS-38.MUSCLE.fa -n Durinskia-baltica-CSIRO_CS-38.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Gambierdiscus-australes-CAWD-149.MUSCLE.fa -n Gambierdiscus-australes-CAWD-149.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Glenodinium-foliaceum-CCAP1116_3.MUSCLE.fa -n Glenodinium-foliaceum-CCAP1116_3.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Gonyaulax-spinifera-CCMP409.MUSCLE.fa -n Gonyaulax-spinifera-CCMP409.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Gymnodinium-catenatum-GC744.MUSCLE.fa -n Gymnodinium-catenatum-GC744.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Heterocapsa-rotundata-SCCAP-K-0483.MUSCLE.fa -n Heterocapsa-rotundata-SCCAP-K-0483.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Heterocapsa-triquestra-CCMP-448.MUSCLE.fa -n Heterocapsa-triquestra-CCMP-448.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Karenia-brevis-CCMP2229.MUSCLE.fa -n Karenia-brevis-CCMP2229.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Karenia-brevis-SP1.MUSCLE.fa -n Karenia-brevis-SP1.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Karenia-brevis-SP3.MUSCLE.fa -n Karenia-brevis-SP3.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Karenia-brevis-Wilson.MUSCLE.fa -n Karenia-brevis-Wilson.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Karlodinium-micrum-CCMP2283.MUSCLE.fa -n Karlodinium-micrum-CCMP2283.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Kryptoperidinium-foliaceum-CCMP1326.MUSCLE.fa -n Kryptoperidinium-foliaceum-CCMP1326.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Lingulodinium-polyedra-CCMP1738.MUSCLE.fa -n Lingulodinium-polyedra-CCMP1738.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Oxyrrhis-marina.MUSCLE.fa -n Oxyrrhis-marina.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Oxyrrhis-marina-CCMP1795.MUSCLE.fa -n Oxyrrhis-marina-CCMP1795.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Oxyrrhis-marina-LB1974.MUSCLE.fa -n Oxyrrhis-marina-LB1974.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Pelagodinium-beii-RCC1491.MUSCLE.fa -n Pelagodinium-beii-RCC1491.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Peridinium-aciculiferum-PAER_2.MUSCLE.fa -n Peridinium-aciculiferum-PAER_2.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Polarella-glacialis-CCMP-1383.MUSCLE.fa -n Polarella-glacialis-CCMP-1383.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Prorocentrum-minimum-CCMP1329.MUSCLE.fa -n Prorocentrum-minimum-CCMP1329.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Prorocentrum-minimum-CCMP2233.MUSCLE.fa -n Prorocentrum-minimum-CCMP2233.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Protoceratium-reticulatum-CCCM-535-CCMP-1889.MUSCLE.fa -n Protoceratium-reticulatum-CCCM-535-CCMP-1889.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Pyrodinium-bahamense-pbaha01.MUSCLE.fa -n Pyrodinium-bahamense-pbaha01.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Scrippsiella-hangoei_like-SHHI_4.MUSCLE.fa -n Scrippsiella-hangoei_like-SHHI_4.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Scrippsiella-hangoei-SHTV5.MUSCLE.fa -n Scrippsiella-hangoei-SHTV5.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Scrippsiella-trochoidea-CCMP3099.MUSCLE.fa -n Scrippsiella-trochoidea-CCMP3099.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Symbiodinium-kawagutii-CCMP2468.MUSCLE.fa -n Symbiodinium-kawagutii-CCMP2468.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Symbiodinium-sp-C1.MUSCLE.fa -n Symbiodinium-sp-C1.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Symbiodinium-sp-C15.MUSCLE.fa -n Symbiodinium-sp-C15.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Symbiodinium-sp-CCMP2430.MUSCLE.fa -n Symbiodinium-sp-CCMP2430.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Symbiodinium-sp-Mp.MUSCLE.fa -n Symbiodinium-sp-Mp.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Togula-jolla-CCCM-725.MUSCLE.fa -n Togula-jolla-CCCM-725.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345
cd /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML; module load raxml/8.0.26; raxml -f a -s Noctiluca-scintillans-Unknown.MUSCLE.fa -n Noctiluca-scintillans-Unknown.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345