/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Ammonia-sp.-Unknown---Ammonia-sp.-Unknown.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Ammonia-sp.-Unknown---Ammonia-sp.-Unknown.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Chattonella-subsalsa-CCMP2191---Chattonella-subsalsa-CCMP2191.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Chattonella-subsalsa-CCMP2191---Chattonella-subsalsa-CCMP2191.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Exanthemachrysis-gayraliae-RCC1523---Exanthemachrysis-gayraliae-RCC1523.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Exanthemachrysis-gayraliae-RCC1523---Exanthemachrysis-gayraliae-RCC1523.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Fibrocapsa-japonica-CCMP1661---Fibrocapsa-japonica-CCMP1661.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Fibrocapsa-japonica-CCMP1661---Fibrocapsa-japonica-CCMP1661.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Goniomonas-pacifica-CCMP1869---Goniomonas-pacifica-CCMP1869.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Goniomonas-pacifica-CCMP1869---Goniomonas-pacifica-CCMP1869.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Hemiselmis-andersenii-CCMP644---Hemiselmis-andersenii-CCMP644.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Hemiselmis-andersenii-CCMP644---Hemiselmis-andersenii-CCMP644.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Hemiselmis-rufescens-PCC563---Hemiselmis-rufescens-PCC563.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Hemiselmis-rufescens-PCC563---Hemiselmis-rufescens-PCC563.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Hemiselmis-tepida-CCMP443---Hemiselmis-tepida-CCMP443.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Hemiselmis-tepida-CCMP443---Hemiselmis-tepida-CCMP443.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Hemiselmis-viresens-PCC157---Hemiselmis-viresens-PCC157.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Hemiselmis-viresens-PCC157---Hemiselmis-viresens-PCC157.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Isochrysis-galbana-CCMP1323---Isochrysis-galbana-CCMP1323.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Isochrysis-galbana-CCMP1323---Isochrysis-galbana-CCMP1323.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Isochrysis-sp-CCMP1244---Isochrysis-sp-CCMP1244.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Isochrysis-sp-CCMP1244---Isochrysis-sp-CCMP1244.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Isochrysis-sp-CCMP1324---Isochrysis-sp-CCMP1324.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Isochrysis-sp-CCMP1324---Isochrysis-sp-CCMP1324.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Pavlova-sp-CCMP459---Pavlova-sp-CCMP459.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Pavlova-sp-CCMP459---Pavlova-sp-CCMP459.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Percolomonas-cosmopolitus-AE-1-ATCC-50343---Percolomonas-cosmopolitus-AE-1-ATCC-50343.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Percolomonas-cosmopolitus-AE-1-ATCC-50343---Percolomonas-cosmopolitus-AE-1-ATCC-50343.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Percolomonas-cosmopolitus-WS---Percolomonas-cosmopolitus-WS.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Percolomonas-cosmopolitus-WS---Percolomonas-cosmopolitus-WS.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Platyophrya-macrostoma-WH---Platyophrya-macrostoma-WH.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Platyophrya-macrostoma-WH---Platyophrya-macrostoma-WH.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Protocruzia-adherens-Boccale---Protocruzia-adherens-Boccale.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Protocruzia-adherens-Boccale---Protocruzia-adherens-Boccale.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Pyramimonas-parkeae-CCMP726---Pyramimonas-parkeae-CCMP726.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Pyramimonas-parkeae-CCMP726---Pyramimonas-parkeae-CCMP726.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Rhodosorus-marinus-CCMP-769---Rhodosorus-marinus-CCMP-769.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Rhodosorus-marinus-CCMP-769---Rhodosorus-marinus-CCMP-769.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Skeletonema-dohrnii-SkelB---Skeletonema-dohrnii-SkelB.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Skeletonema-dohrnii-SkelB---Skeletonema-dohrnii-SkelB.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Skeletonema-marinoi-SkelA---Skeletonema-marinoi-SkelA.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Skeletonema-marinoi-SkelA---Skeletonema-marinoi-SkelA.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Skeletonema-menzelii-CCMP793---Skeletonema-menzelii-CCMP793.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Skeletonema-menzelii-CCMP793---Skeletonema-menzelii-CCMP793.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Spumella-elongata-CCAP-955-1---Spumella-elongata-CCAP-955-1.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Spumella-elongata-CCAP-955-1---Spumella-elongata-CCAP-955-1.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Strombidinopsis-acuminatum-SPMC142---Strombidinopsis-acuminatum-SPMC142.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Strombidinopsis-acuminatum-SPMC142---Strombidinopsis-acuminatum-SPMC142.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Strombidinopsis-sp-SopsisLIS2011---Strombidinopsis-sp-SopsisLIS2011.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Strombidinopsis-sp-SopsisLIS2011---Strombidinopsis-sp-SopsisLIS2011.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Paraphysomonas-bandaiensis-Caron-Lab-Isolate---Paraphysomonas-bandaiensis-Caron-Lab-Isolate.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Paraphysomonas-bandaiensis-Caron-Lab-Isolate---Paraphysomonas-bandaiensis-Caron-Lab-Isolate.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Paraphysomonas-imperforata-PA2---Paraphysomonas-imperforata-PA2.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Paraphysomonas-imperforata-PA2---Paraphysomonas-imperforata-PA2.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Proboscia-alata-PI_D3---Proboscia-alata-PI_D3.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Proboscia-alata-PI_D3---Proboscia-alata-PI_D3.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Rhizosolenia-setigera-CCMP-1694---Rhizosolenia-setigera-CCMP-1694.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Rhizosolenia-setigera-CCMP-1694---Rhizosolenia-setigera-CCMP-1694.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Dactyliosolen-fragilissimus-Unknown---Dactyliosolen-fragilissimus-Unknown.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Dactyliosolen-fragilissimus-Unknown---Dactyliosolen-fragilissimus-Unknown.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Prymnesium-parvum-Texoma1---Prymnesium-parvum-Texoma1.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Prymnesium-parvum-Texoma1---Prymnesium-parvum-Texoma1.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Imantonia-sp.-RCC918---Imantonia-sp.-RCC918.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Imantonia-sp.-RCC918---Imantonia-sp.-RCC918.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Chrysoculter-rhomboideus-RCC1486---Chrysoculter-rhomboideus-RCC1486.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Chrysoculter-rhomboideus-RCC1486---Chrysoculter-rhomboideus-RCC1486.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Chrysochromulina-ericina-CCMP281---Chrysochromulina-ericina-CCMP281.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Chrysochromulina-ericina-CCMP281---Chrysochromulina-ericina-CCMP281.30bp.end1.22mers.counts.top100.MUSCLE.fa &
/oak/stanford/groups/akundaje/marinovg/programs/muscle3.8.31/muscle3.8.31_i86linux64 -in Original_MMETSP_files---Chrysochromulina-polylepis-CCMP1757---Chrysochromulina-polylepis-CCMP1757.30bp.end1.22mers.counts.top100.fa -out Original_MMETSP_files---Chrysochromulina-polylepis-CCMP1757---Chrysochromulina-polylepis-CCMP1757.30bp.end1.22mers.counts.top100.MUSCLE.fa &