mkdir test_msas
mkdir test_msas/gappyout
mkdir test_msas/strict
mkdir test_msas/strictplus
mkdir test_msas/automated1
mkdir test_msas/nogaps
mkdir test_msas/noallgaps

./source/trimal -in dataset/example.004.AA.fasta -gappyout > test_msas/gappyout/example.004.AA.fasta
./source/trimal -in dataset/example.004.AA.fasta -strict > test_msas/strict/example.004.AA.fasta
./source/trimal -in dataset/example.004.AA.fasta -strictplus > test_msas/strictplus/example.004.AA.fasta
./source/trimal -in dataset/example.004.AA.fasta -automated1 > test_msas/automated1/example.004.AA.fasta
./source/trimal -in dataset/example.004.AA.fasta -nogaps > test_msas/nogaps/example.004.AA.fasta
./source/trimal -in dataset/example.004.AA.fasta -noallgaps > test_msas/noallgaps/example.004.AA.fasta
./source/trimal -in dataset/example.005.AA.fasta -gappyout > test_msas/gappyout/example.005.AA.fasta
./source/trimal -in dataset/example.005.AA.fasta -strict > test_msas/strict/example.005.AA.fasta
./source/trimal -in dataset/example.005.AA.fasta -strictplus > test_msas/strictplus/example.005.AA.fasta
./source/trimal -in dataset/example.005.AA.fasta -automated1 > test_msas/automated1/example.005.AA.fasta
./source/trimal -in dataset/example.005.AA.fasta -nogaps > test_msas/nogaps/example.005.AA.fasta
./source/trimal -in dataset/example.005.AA.fasta -noallgaps > test_msas/noallgaps/example.005.AA.fasta
./source/trimal -in dataset/example.007.AA.fasta -gappyout > test_msas/gappyout/example.007.AA.fasta
./source/trimal -in dataset/example.007.AA.fasta -strict > test_msas/strict/example.007.AA.fasta
./source/trimal -in dataset/example.007.AA.fasta -strictplus > test_msas/strictplus/example.007.AA.fasta
./source/trimal -in dataset/example.007.AA.fasta -automated1 > test_msas/automated1/example.007.AA.fasta
./source/trimal -in dataset/example.007.AA.fasta -nogaps > test_msas/nogaps/example.007.AA.fasta
./source/trimal -in dataset/example.007.AA.fasta -noallgaps > test_msas/noallgaps/example.007.AA.fasta
./source/trimal -in dataset/example.009.AA.fasta -gappyout > test_msas/gappyout/example.009.AA.fasta
./source/trimal -in dataset/example.009.AA.fasta -strict > test_msas/strict/example.009.AA.fasta
./source/trimal -in dataset/example.009.AA.fasta -strictplus > test_msas/strictplus/example.009.AA.fasta
./source/trimal -in dataset/example.009.AA.fasta -automated1 > test_msas/automated1/example.009.AA.fasta
./source/trimal -in dataset/example.009.AA.fasta -nogaps > test_msas/nogaps/example.009.AA.fasta
./source/trimal -in dataset/example.009.AA.fasta -noallgaps > test_msas/noallgaps/example.009.AA.fasta
./source/trimal -in dataset/example.010.AA.fasta -gappyout > test_msas/gappyout/example.010.AA.fasta
./source/trimal -in dataset/example.010.AA.fasta -strict > test_msas/strict/example.010.AA.fasta
./source/trimal -in dataset/example.010.AA.fasta -strictplus > test_msas/strictplus/example.010.AA.fasta
./source/trimal -in dataset/example.010.AA.fasta -automated1 > test_msas/automated1/example.010.AA.fasta
./source/trimal -in dataset/example.010.AA.fasta -nogaps > test_msas/nogaps/example.010.AA.fasta
./source/trimal -in dataset/example.010.AA.fasta -noallgaps > test_msas/noallgaps/example.010.AA.fasta
./source/trimal -in dataset/example.011.AA.YKL197C.fasta -gappyout > test_msas/gappyout/example.011.AA.YKL197C.fasta
./source/trimal -in dataset/example.011.AA.YKL197C.fasta -strict > test_msas/strict/example.011.AA.YKL197C.fasta
./source/trimal -in dataset/example.011.AA.YKL197C.fasta -strictplus > test_msas/strictplus/example.011.AA.YKL197C.fasta
./source/trimal -in dataset/example.011.AA.YKL197C.fasta -automated1 > test_msas/automated1/example.011.AA.YKL197C.fasta
./source/trimal -in dataset/example.011.AA.YKL197C.fasta -nogaps > test_msas/nogaps/example.011.AA.YKL197C.fasta
./source/trimal -in dataset/example.011.AA.YKL197C.fasta -noallgaps > test_msas/noallgaps/example.011.AA.YKL197C.fasta
./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas/gappyout/example.014.AA.EggNOG.COG0591.fasta
./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -strict > test_msas/strict/example.014.AA.EggNOG.COG0591.fasta
./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas/strictplus/example.014.AA.EggNOG.COG0591.fasta
./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas/automated1/example.014.AA.EggNOG.COG0591.fasta
./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas/nogaps/example.014.AA.EggNOG.COG0591.fasta
./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas/noallgaps/example.014.AA.EggNOG.COG0591.fasta
./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas/gappyout/example.015.AA.bctoNOG.ENOG41099F3.fasta
./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas/strict/example.015.AA.bctoNOG.ENOG41099F3.fasta
./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas/strictplus/example.015.AA.bctoNOG.ENOG41099F3.fasta
./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas/automated1/example.015.AA.bctoNOG.ENOG41099F3.fasta
./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas/nogaps/example.015.AA.bctoNOG.ENOG41099F3.fasta
./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas/noallgaps/example.015.AA.bctoNOG.ENOG41099F3.fasta
./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas/gappyout/example.016.AA.bctoNOG.ENOG41099FB.fasta
./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas/strict/example.016.AA.bctoNOG.ENOG41099FB.fasta
./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas/strictplus/example.016.AA.bctoNOG.ENOG41099FB.fasta
./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas/automated1/example.016.AA.bctoNOG.ENOG41099FB.fasta
./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas/nogaps/example.016.AA.bctoNOG.ENOG41099FB.fasta
./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas/noallgaps/example.016.AA.bctoNOG.ENOG41099FB.fasta
./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas/gappyout/example.017.AA.bctoNOG.ENOG41099FJ.fasta
./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas/strict/example.017.AA.bctoNOG.ENOG41099FJ.fasta
./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas/strictplus/example.017.AA.bctoNOG.ENOG41099FJ.fasta
./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas/automated1/example.017.AA.bctoNOG.ENOG41099FJ.fasta
./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas/nogaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta
./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas/noallgaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta
./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas/gappyout/example.018.AA.bctoNOG.ENOG41099FV.fasta
./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas/strict/example.018.AA.bctoNOG.ENOG41099FV.fasta
./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas/strictplus/example.018.AA.bctoNOG.ENOG41099FV.fasta
./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas/automated1/example.018.AA.bctoNOG.ENOG41099FV.fasta
./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas/nogaps/example.018.AA.bctoNOG.ENOG41099FV.fasta
./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas/noallgaps/example.018.AA.bctoNOG.ENOG41099FV.fasta
./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas/gappyout/example.019.AA.bctoNOG.ENOG41099HI.fasta
./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas/strict/example.019.AA.bctoNOG.ENOG41099HI.fasta
./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas/strictplus/example.019.AA.bctoNOG.ENOG41099HI.fasta
./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas/automated1/example.019.AA.bctoNOG.ENOG41099HI.fasta
./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas/nogaps/example.019.AA.bctoNOG.ENOG41099HI.fasta
./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas/noallgaps/example.019.AA.bctoNOG.ENOG41099HI.fasta
./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas/gappyout/example.020.AA.bctoNOG.ENOG41099HN.fasta
./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas/strict/example.020.AA.bctoNOG.ENOG41099HN.fasta
./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas/strictplus/example.020.AA.bctoNOG.ENOG41099HN.fasta
./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas/automated1/example.020.AA.bctoNOG.ENOG41099HN.fasta
./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas/nogaps/example.020.AA.bctoNOG.ENOG41099HN.fasta
./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas/noallgaps/example.020.AA.bctoNOG.ENOG41099HN.fasta
./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas/gappyout/example.021.AA.bctoNOG.ENOG41099I5.fasta
./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas/strict/example.021.AA.bctoNOG.ENOG41099I5.fasta
./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas/strictplus/example.021.AA.bctoNOG.ENOG41099I5.fasta
./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas/automated1/example.021.AA.bctoNOG.ENOG41099I5.fasta
./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas/nogaps/example.021.AA.bctoNOG.ENOG41099I5.fasta
./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas/noallgaps/example.021.AA.bctoNOG.ENOG41099I5.fasta
./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas/gappyout/example.022.AA.bctoNOG.ENOG41099IZ.fasta
./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas/strict/example.022.AA.bctoNOG.ENOG41099IZ.fasta
./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas/strictplus/example.022.AA.bctoNOG.ENOG41099IZ.fasta
./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas/automated1/example.022.AA.bctoNOG.ENOG41099IZ.fasta
./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas/nogaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta
./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas/noallgaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta
./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas/gappyout/example.023.AA.bctoNOG.ENOG41099K3.fasta
./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas/strict/example.023.AA.bctoNOG.ENOG41099K3.fasta
./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas/strictplus/example.023.AA.bctoNOG.ENOG41099K3.fasta
./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas/automated1/example.023.AA.bctoNOG.ENOG41099K3.fasta
./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas/nogaps/example.023.AA.bctoNOG.ENOG41099K3.fasta
./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas/noallgaps/example.023.AA.bctoNOG.ENOG41099K3.fasta
./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas/gappyout/example.024.AA.bctoNOG.ENOG41099KM.fasta
./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas/strict/example.024.AA.bctoNOG.ENOG41099KM.fasta
./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas/strictplus/example.024.AA.bctoNOG.ENOG41099KM.fasta
./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas/automated1/example.024.AA.bctoNOG.ENOG41099KM.fasta
./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas/nogaps/example.024.AA.bctoNOG.ENOG41099KM.fasta
./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas/noallgaps/example.024.AA.bctoNOG.ENOG41099KM.fasta
./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas/gappyout/example.025.AA.bctoNOG.ENOG41099KP.fasta
./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas/strict/example.025.AA.bctoNOG.ENOG41099KP.fasta
./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas/strictplus/example.025.AA.bctoNOG.ENOG41099KP.fasta
./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas/automated1/example.025.AA.bctoNOG.ENOG41099KP.fasta
./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas/nogaps/example.025.AA.bctoNOG.ENOG41099KP.fasta
./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas/noallgaps/example.025.AA.bctoNOG.ENOG41099KP.fasta
./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas/gappyout/example.026.AA.bctoNOG.ENOG41099MV.fasta
./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas/strict/example.026.AA.bctoNOG.ENOG41099MV.fasta
./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas/strictplus/example.026.AA.bctoNOG.ENOG41099MV.fasta
./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas/automated1/example.026.AA.bctoNOG.ENOG41099MV.fasta
./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas/nogaps/example.026.AA.bctoNOG.ENOG41099MV.fasta
./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas/noallgaps/example.026.AA.bctoNOG.ENOG41099MV.fasta
./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas/gappyout/example.027.AA.bctoNOG.ENOG41099NY.fasta
./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas/strict/example.027.AA.bctoNOG.ENOG41099NY.fasta
./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas/strictplus/example.027.AA.bctoNOG.ENOG41099NY.fasta
./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas/automated1/example.027.AA.bctoNOG.ENOG41099NY.fasta
./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas/nogaps/example.027.AA.bctoNOG.ENOG41099NY.fasta
./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas/noallgaps/example.027.AA.bctoNOG.ENOG41099NY.fasta
./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas/gappyout/example.028.AA.bctoNOG.ENOG41099PA.fasta
./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas/strict/example.028.AA.bctoNOG.ENOG41099PA.fasta
./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas/strictplus/example.028.AA.bctoNOG.ENOG41099PA.fasta
./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas/automated1/example.028.AA.bctoNOG.ENOG41099PA.fasta
./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas/nogaps/example.028.AA.bctoNOG.ENOG41099PA.fasta
./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas/noallgaps/example.028.AA.bctoNOG.ENOG41099PA.fasta
./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas/gappyout/example.029.AA.bctoNOG.ENOG41099Q3.fasta
./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas/strict/example.029.AA.bctoNOG.ENOG41099Q3.fasta
./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas/strictplus/example.029.AA.bctoNOG.ENOG41099Q3.fasta
./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas/automated1/example.029.AA.bctoNOG.ENOG41099Q3.fasta
./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas/nogaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta
./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas/noallgaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta
./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas/gappyout/example.030.AA.bctoNOG.ENOG41099RG.fasta
./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas/strict/example.030.AA.bctoNOG.ENOG41099RG.fasta
./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas/strictplus/example.030.AA.bctoNOG.ENOG41099RG.fasta
./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas/automated1/example.030.AA.bctoNOG.ENOG41099RG.fasta
./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas/nogaps/example.030.AA.bctoNOG.ENOG41099RG.fasta
./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas/noallgaps/example.030.AA.bctoNOG.ENOG41099RG.fasta
./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas/gappyout/example.031.AA.bctoNOG.ENOG41099UK.fasta
./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas/strict/example.031.AA.bctoNOG.ENOG41099UK.fasta
./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas/strictplus/example.031.AA.bctoNOG.ENOG41099UK.fasta
./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas/automated1/example.031.AA.bctoNOG.ENOG41099UK.fasta
./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas/nogaps/example.031.AA.bctoNOG.ENOG41099UK.fasta
./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas/noallgaps/example.031.AA.bctoNOG.ENOG41099UK.fasta
./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas/gappyout/example.032.AA.bctoNOG.ENOG41099UW.fasta
./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas/strict/example.032.AA.bctoNOG.ENOG41099UW.fasta
./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas/strictplus/example.032.AA.bctoNOG.ENOG41099UW.fasta
./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas/automated1/example.032.AA.bctoNOG.ENOG41099UW.fasta
./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas/nogaps/example.032.AA.bctoNOG.ENOG41099UW.fasta
./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas/noallgaps/example.032.AA.bctoNOG.ENOG41099UW.fasta
./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas/gappyout/example.033.AA.bctoNOG.ENOG41099VK.fasta
./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas/strict/example.033.AA.bctoNOG.ENOG41099VK.fasta
./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas/strictplus/example.033.AA.bctoNOG.ENOG41099VK.fasta
./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas/automated1/example.033.AA.bctoNOG.ENOG41099VK.fasta
./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas/nogaps/example.033.AA.bctoNOG.ENOG41099VK.fasta
./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas/noallgaps/example.033.AA.bctoNOG.ENOG41099VK.fasta
./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas/gappyout/example.034.AA.bctoNOG.ENOG41099WA.fasta
./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas/strict/example.034.AA.bctoNOG.ENOG41099WA.fasta
./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas/strictplus/example.034.AA.bctoNOG.ENOG41099WA.fasta
./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas/automated1/example.034.AA.bctoNOG.ENOG41099WA.fasta
./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas/nogaps/example.034.AA.bctoNOG.ENOG41099WA.fasta
./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas/noallgaps/example.034.AA.bctoNOG.ENOG41099WA.fasta
./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas/gappyout/example.035.AA.bctoNOG.ENOG41099WF.fasta
./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas/strict/example.035.AA.bctoNOG.ENOG41099WF.fasta
./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas/strictplus/example.035.AA.bctoNOG.ENOG41099WF.fasta
./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas/automated1/example.035.AA.bctoNOG.ENOG41099WF.fasta
./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas/nogaps/example.035.AA.bctoNOG.ENOG41099WF.fasta
./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas/noallgaps/example.035.AA.bctoNOG.ENOG41099WF.fasta
./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas/gappyout/example.036.AA.bctoNOG.ENOG41099XJ.fasta
./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas/strict/example.036.AA.bctoNOG.ENOG41099XJ.fasta
./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas/strictplus/example.036.AA.bctoNOG.ENOG41099XJ.fasta
./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas/automated1/example.036.AA.bctoNOG.ENOG41099XJ.fasta
./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas/nogaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta
./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas/noallgaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta
./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas/gappyout/example.037.AA.bctoNOG.ENOG41099XP.fasta
./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas/strict/example.037.AA.bctoNOG.ENOG41099XP.fasta
./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas/strictplus/example.037.AA.bctoNOG.ENOG41099XP.fasta
./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas/automated1/example.037.AA.bctoNOG.ENOG41099XP.fasta
./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas/nogaps/example.037.AA.bctoNOG.ENOG41099XP.fasta
./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas/noallgaps/example.037.AA.bctoNOG.ENOG41099XP.fasta
./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas/gappyout/example.038.AA.bctoNOG.ENOG41099Y4.fasta
./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas/strict/example.038.AA.bctoNOG.ENOG41099Y4.fasta
./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas/strictplus/example.038.AA.bctoNOG.ENOG41099Y4.fasta
./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas/automated1/example.038.AA.bctoNOG.ENOG41099Y4.fasta
./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas/nogaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta
./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas/noallgaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta
./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas/gappyout/example.039.AA.bctoNOG.ENOG41099YD.fasta
./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas/strict/example.039.AA.bctoNOG.ENOG41099YD.fasta
./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas/strictplus/example.039.AA.bctoNOG.ENOG41099YD.fasta
./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas/automated1/example.039.AA.bctoNOG.ENOG41099YD.fasta
./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas/nogaps/example.039.AA.bctoNOG.ENOG41099YD.fasta
./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas/noallgaps/example.039.AA.bctoNOG.ENOG41099YD.fasta
./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas/gappyout/example.040.AA.bctoNOG.ENOG4109A32.fasta
./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas/strict/example.040.AA.bctoNOG.ENOG4109A32.fasta
./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas/strictplus/example.040.AA.bctoNOG.ENOG4109A32.fasta
./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas/automated1/example.040.AA.bctoNOG.ENOG4109A32.fasta
./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas/nogaps/example.040.AA.bctoNOG.ENOG4109A32.fasta
./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas/noallgaps/example.040.AA.bctoNOG.ENOG4109A32.fasta
./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas/gappyout/example.041.AA.bctoNOG.ENOG4109A5T.fasta
./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas/strict/example.041.AA.bctoNOG.ENOG4109A5T.fasta
./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas/strictplus/example.041.AA.bctoNOG.ENOG4109A5T.fasta
./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas/automated1/example.041.AA.bctoNOG.ENOG4109A5T.fasta
./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas/nogaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta
./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas/noallgaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta
./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas/gappyout/example.042.AA.bctoNOG.ENOG4109A9M.fasta
./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas/strict/example.042.AA.bctoNOG.ENOG4109A9M.fasta
./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas/strictplus/example.042.AA.bctoNOG.ENOG4109A9M.fasta
./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas/automated1/example.042.AA.bctoNOG.ENOG4109A9M.fasta
./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas/nogaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta
./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas/noallgaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta
./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas/gappyout/example.043.AA.bctoNOG.ENOG4109ADN.fasta
./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas/strict/example.043.AA.bctoNOG.ENOG4109ADN.fasta
./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas/strictplus/example.043.AA.bctoNOG.ENOG4109ADN.fasta
./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas/automated1/example.043.AA.bctoNOG.ENOG4109ADN.fasta
./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas/nogaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta
./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas/noallgaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta
./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas/gappyout/example.044.AA.bctoNOG.ENOG4109AED.fasta
./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas/strict/example.044.AA.bctoNOG.ENOG4109AED.fasta
./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas/strictplus/example.044.AA.bctoNOG.ENOG4109AED.fasta
./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas/automated1/example.044.AA.bctoNOG.ENOG4109AED.fasta
./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas/nogaps/example.044.AA.bctoNOG.ENOG4109AED.fasta
./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas/noallgaps/example.044.AA.bctoNOG.ENOG4109AED.fasta
./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas/gappyout/example.045.AA.bctoNOG.ENOG4109AGT.fasta
./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas/strict/example.045.AA.bctoNOG.ENOG4109AGT.fasta
./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas/strictplus/example.045.AA.bctoNOG.ENOG4109AGT.fasta
./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas/automated1/example.045.AA.bctoNOG.ENOG4109AGT.fasta
./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas/nogaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta
./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas/noallgaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta
./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas/gappyout/example.046.AA.bctoNOG.ENOG4109AGW.fasta
./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas/strict/example.046.AA.bctoNOG.ENOG4109AGW.fasta
./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas/strictplus/example.046.AA.bctoNOG.ENOG4109AGW.fasta
./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas/automated1/example.046.AA.bctoNOG.ENOG4109AGW.fasta
./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas/nogaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta
./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas/noallgaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta
./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas/gappyout/example.047.AA.bctoNOG.ENOG4109AIC.fasta
./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas/strict/example.047.AA.bctoNOG.ENOG4109AIC.fasta
./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas/strictplus/example.047.AA.bctoNOG.ENOG4109AIC.fasta
./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas/automated1/example.047.AA.bctoNOG.ENOG4109AIC.fasta
./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas/nogaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta
./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas/noallgaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta
./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas/gappyout/example.048.AA.bctoNOG.ENOG4109AJ3.fasta
./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas/strict/example.048.AA.bctoNOG.ENOG4109AJ3.fasta
./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas/strictplus/example.048.AA.bctoNOG.ENOG4109AJ3.fasta
./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas/automated1/example.048.AA.bctoNOG.ENOG4109AJ3.fasta
./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas/nogaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta
./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas/noallgaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta
./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas/gappyout/example.049.AA.bctoNOG.ENOG4109AY5.fasta
./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas/strict/example.049.AA.bctoNOG.ENOG4109AY5.fasta
./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas/strictplus/example.049.AA.bctoNOG.ENOG4109AY5.fasta
./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas/automated1/example.049.AA.bctoNOG.ENOG4109AY5.fasta
./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas/nogaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta
./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas/noallgaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta
./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas/gappyout/example.050.AA.bctoNOG.ENOG4109B8Z.fasta
./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas/strict/example.050.AA.bctoNOG.ENOG4109B8Z.fasta
./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas/strictplus/example.050.AA.bctoNOG.ENOG4109B8Z.fasta
./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas/automated1/example.050.AA.bctoNOG.ENOG4109B8Z.fasta
./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas/nogaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta
./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas/noallgaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta
./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas/gappyout/example.051.AA.bctoNOG.ENOG4109BCJ.fasta
./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas/strict/example.051.AA.bctoNOG.ENOG4109BCJ.fasta
./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas/strictplus/example.051.AA.bctoNOG.ENOG4109BCJ.fasta
./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas/automated1/example.051.AA.bctoNOG.ENOG4109BCJ.fasta
./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas/nogaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta
./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas/noallgaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta
./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas/gappyout/example.052.AA.bctoNOG.ENOG4109CTU.fasta
./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas/strict/example.052.AA.bctoNOG.ENOG4109CTU.fasta
./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas/strictplus/example.052.AA.bctoNOG.ENOG4109CTU.fasta
./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas/automated1/example.052.AA.bctoNOG.ENOG4109CTU.fasta
./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas/nogaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta
./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas/noallgaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta
./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas/gappyout/example.053.AA.bctoNOG.ENOG4109CVC.fasta
./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas/strict/example.053.AA.bctoNOG.ENOG4109CVC.fasta
./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas/strictplus/example.053.AA.bctoNOG.ENOG4109CVC.fasta
./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas/automated1/example.053.AA.bctoNOG.ENOG4109CVC.fasta
./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas/nogaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta
./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas/noallgaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta
./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas/gappyout/example.054.AA.bctoNOG.ENOG4109FIT.fasta
./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas/strict/example.054.AA.bctoNOG.ENOG4109FIT.fasta
./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas/strictplus/example.054.AA.bctoNOG.ENOG4109FIT.fasta
./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas/automated1/example.054.AA.bctoNOG.ENOG4109FIT.fasta
./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas/nogaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta
./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas/noallgaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta
./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas/gappyout/example.055.AA.bctoNOG.ENOG4109GY9.fasta
./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas/strict/example.055.AA.bctoNOG.ENOG4109GY9.fasta
./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas/strictplus/example.055.AA.bctoNOG.ENOG4109GY9.fasta
./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas/automated1/example.055.AA.bctoNOG.ENOG4109GY9.fasta
./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas/nogaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta
./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas/noallgaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta
./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas/gappyout/example.056.AA.bctoNOG.ENOG4109IPJ.fasta
./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas/strict/example.056.AA.bctoNOG.ENOG4109IPJ.fasta
./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas/strictplus/example.056.AA.bctoNOG.ENOG4109IPJ.fasta
./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas/automated1/example.056.AA.bctoNOG.ENOG4109IPJ.fasta
./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas/nogaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta
./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas/noallgaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta
./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas/gappyout/example.057.AA.bctoNOG.ENOG4109SZ2.fasta
./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas/strict/example.057.AA.bctoNOG.ENOG4109SZ2.fasta
./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas/strictplus/example.057.AA.bctoNOG.ENOG4109SZ2.fasta
./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas/automated1/example.057.AA.bctoNOG.ENOG4109SZ2.fasta
./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas/nogaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta
./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas/noallgaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta
./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas/gappyout/example.058.AA.strNOG.ENOG411BBR6.fasta
./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas/strict/example.058.AA.strNOG.ENOG411BBR6.fasta
./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas/strictplus/example.058.AA.strNOG.ENOG411BBR6.fasta
./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas/automated1/example.058.AA.strNOG.ENOG411BBR6.fasta
./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas/nogaps/example.058.AA.strNOG.ENOG411BBR6.fasta
./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas/noallgaps/example.058.AA.strNOG.ENOG411BBR6.fasta
./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas/gappyout/example.059.AA.strNOG.ENOG411BBRR.fasta
./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas/strict/example.059.AA.strNOG.ENOG411BBRR.fasta
./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas/strictplus/example.059.AA.strNOG.ENOG411BBRR.fasta
./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas/automated1/example.059.AA.strNOG.ENOG411BBRR.fasta
./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas/nogaps/example.059.AA.strNOG.ENOG411BBRR.fasta
./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas/noallgaps/example.059.AA.strNOG.ENOG411BBRR.fasta
./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas/gappyout/example.060.AA.strNOG.ENOG411BBWK.fasta
./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas/strict/example.060.AA.strNOG.ENOG411BBWK.fasta
./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas/strictplus/example.060.AA.strNOG.ENOG411BBWK.fasta
./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas/automated1/example.060.AA.strNOG.ENOG411BBWK.fasta
./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas/nogaps/example.060.AA.strNOG.ENOG411BBWK.fasta
./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas/noallgaps/example.060.AA.strNOG.ENOG411BBWK.fasta
./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas/gappyout/example.061.AA.strNOG.ENOG411BCDZ.fasta
./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas/strict/example.061.AA.strNOG.ENOG411BCDZ.fasta
./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas/strictplus/example.061.AA.strNOG.ENOG411BCDZ.fasta
./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas/automated1/example.061.AA.strNOG.ENOG411BCDZ.fasta
./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas/nogaps/example.061.AA.strNOG.ENOG411BCDZ.fasta
./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas/noallgaps/example.061.AA.strNOG.ENOG411BCDZ.fasta
./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas/gappyout/example.062.AA.strNOG.ENOG411BCX3.fasta
./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas/strict/example.062.AA.strNOG.ENOG411BCX3.fasta
./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas/strictplus/example.062.AA.strNOG.ENOG411BCX3.fasta
./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas/automated1/example.062.AA.strNOG.ENOG411BCX3.fasta
./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas/nogaps/example.062.AA.strNOG.ENOG411BCX3.fasta
./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas/noallgaps/example.062.AA.strNOG.ENOG411BCX3.fasta
./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas/gappyout/example.063.AA.strNOG.ENOG411BDBU.fasta
./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas/strict/example.063.AA.strNOG.ENOG411BDBU.fasta
./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas/strictplus/example.063.AA.strNOG.ENOG411BDBU.fasta
./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas/automated1/example.063.AA.strNOG.ENOG411BDBU.fasta
./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas/nogaps/example.063.AA.strNOG.ENOG411BDBU.fasta
./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas/noallgaps/example.063.AA.strNOG.ENOG411BDBU.fasta
./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas/gappyout/example.064.AA.strNOG.ENOG411BDKC.fasta
./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas/strict/example.064.AA.strNOG.ENOG411BDKC.fasta
./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas/strictplus/example.064.AA.strNOG.ENOG411BDKC.fasta
./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas/automated1/example.064.AA.strNOG.ENOG411BDKC.fasta
./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas/nogaps/example.064.AA.strNOG.ENOG411BDKC.fasta
./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas/noallgaps/example.064.AA.strNOG.ENOG411BDKC.fasta
./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas/gappyout/example.065.AA.strNOG.ENOG411BDSZ.fasta
./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas/strict/example.065.AA.strNOG.ENOG411BDSZ.fasta
./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas/strictplus/example.065.AA.strNOG.ENOG411BDSZ.fasta
./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas/automated1/example.065.AA.strNOG.ENOG411BDSZ.fasta
./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas/nogaps/example.065.AA.strNOG.ENOG411BDSZ.fasta
./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas/noallgaps/example.065.AA.strNOG.ENOG411BDSZ.fasta
./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas/gappyout/example.066.AA.strNOG.ENOG411BDUE.fasta
./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas/strict/example.066.AA.strNOG.ENOG411BDUE.fasta
./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas/strictplus/example.066.AA.strNOG.ENOG411BDUE.fasta
./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas/automated1/example.066.AA.strNOG.ENOG411BDUE.fasta
./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas/nogaps/example.066.AA.strNOG.ENOG411BDUE.fasta
./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas/noallgaps/example.066.AA.strNOG.ENOG411BDUE.fasta
./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas/gappyout/example.067.AA.strNOG.ENOG411BDX3.fasta
./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas/strict/example.067.AA.strNOG.ENOG411BDX3.fasta
./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas/strictplus/example.067.AA.strNOG.ENOG411BDX3.fasta
./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas/automated1/example.067.AA.strNOG.ENOG411BDX3.fasta
./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas/nogaps/example.067.AA.strNOG.ENOG411BDX3.fasta
./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas/noallgaps/example.067.AA.strNOG.ENOG411BDX3.fasta
./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas/gappyout/example.068.AA.strNOG.ENOG411BE45.fasta
./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas/strict/example.068.AA.strNOG.ENOG411BE45.fasta
./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas/strictplus/example.068.AA.strNOG.ENOG411BE45.fasta
./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas/automated1/example.068.AA.strNOG.ENOG411BE45.fasta
./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas/nogaps/example.068.AA.strNOG.ENOG411BE45.fasta
./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas/noallgaps/example.068.AA.strNOG.ENOG411BE45.fasta
./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas/gappyout/example.069.AA.strNOG.ENOG411BE8B.fasta
./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas/strict/example.069.AA.strNOG.ENOG411BE8B.fasta
./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas/strictplus/example.069.AA.strNOG.ENOG411BE8B.fasta
./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas/automated1/example.069.AA.strNOG.ENOG411BE8B.fasta
./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas/nogaps/example.069.AA.strNOG.ENOG411BE8B.fasta
./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas/noallgaps/example.069.AA.strNOG.ENOG411BE8B.fasta
./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas/gappyout/example.070.AA.strNOG.ENOG411BEUV.fasta
./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas/strict/example.070.AA.strNOG.ENOG411BEUV.fasta
./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas/strictplus/example.070.AA.strNOG.ENOG411BEUV.fasta
./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas/automated1/example.070.AA.strNOG.ENOG411BEUV.fasta
./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas/nogaps/example.070.AA.strNOG.ENOG411BEUV.fasta
./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas/noallgaps/example.070.AA.strNOG.ENOG411BEUV.fasta
./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas/gappyout/example.071.AA.strNOG.ENOG411BEZ0.fasta
./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas/strict/example.071.AA.strNOG.ENOG411BEZ0.fasta
./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas/strictplus/example.071.AA.strNOG.ENOG411BEZ0.fasta
./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas/automated1/example.071.AA.strNOG.ENOG411BEZ0.fasta
./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas/nogaps/example.071.AA.strNOG.ENOG411BEZ0.fasta
./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas/noallgaps/example.071.AA.strNOG.ENOG411BEZ0.fasta
./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas/gappyout/example.072.AA.strNOG.ENOG411BF1S.fasta
./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas/strict/example.072.AA.strNOG.ENOG411BF1S.fasta
./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas/strictplus/example.072.AA.strNOG.ENOG411BF1S.fasta
./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas/automated1/example.072.AA.strNOG.ENOG411BF1S.fasta
./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas/nogaps/example.072.AA.strNOG.ENOG411BF1S.fasta
./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas/noallgaps/example.072.AA.strNOG.ENOG411BF1S.fasta
./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas/gappyout/example.073.AA.strNOG.ENOG411BFCW.fasta
./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas/strict/example.073.AA.strNOG.ENOG411BFCW.fasta
./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas/strictplus/example.073.AA.strNOG.ENOG411BFCW.fasta
./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas/automated1/example.073.AA.strNOG.ENOG411BFCW.fasta
./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas/nogaps/example.073.AA.strNOG.ENOG411BFCW.fasta
./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas/noallgaps/example.073.AA.strNOG.ENOG411BFCW.fasta
./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas/gappyout/example.074.AA.strNOG.ENOG411BFPF.fasta
./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas/strict/example.074.AA.strNOG.ENOG411BFPF.fasta
./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas/strictplus/example.074.AA.strNOG.ENOG411BFPF.fasta
./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas/automated1/example.074.AA.strNOG.ENOG411BFPF.fasta
./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas/nogaps/example.074.AA.strNOG.ENOG411BFPF.fasta
./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas/noallgaps/example.074.AA.strNOG.ENOG411BFPF.fasta
./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas/gappyout/example.075.AA.strNOG.ENOG411BFQS.fasta
./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas/strict/example.075.AA.strNOG.ENOG411BFQS.fasta
./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas/strictplus/example.075.AA.strNOG.ENOG411BFQS.fasta
./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas/automated1/example.075.AA.strNOG.ENOG411BFQS.fasta
./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas/nogaps/example.075.AA.strNOG.ENOG411BFQS.fasta
./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas/noallgaps/example.075.AA.strNOG.ENOG411BFQS.fasta
./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas/gappyout/example.076.AA.strNOG.ENOG411BH75.fasta
./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas/strict/example.076.AA.strNOG.ENOG411BH75.fasta
./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas/strictplus/example.076.AA.strNOG.ENOG411BH75.fasta
./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas/automated1/example.076.AA.strNOG.ENOG411BH75.fasta
./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas/nogaps/example.076.AA.strNOG.ENOG411BH75.fasta
./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas/noallgaps/example.076.AA.strNOG.ENOG411BH75.fasta
./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas/gappyout/example.077.AA.strNOG.ENOG411BH79.fasta
./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas/strict/example.077.AA.strNOG.ENOG411BH79.fasta
./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas/strictplus/example.077.AA.strNOG.ENOG411BH79.fasta
./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas/automated1/example.077.AA.strNOG.ENOG411BH79.fasta
./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas/nogaps/example.077.AA.strNOG.ENOG411BH79.fasta
./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas/noallgaps/example.077.AA.strNOG.ENOG411BH79.fasta
./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas/gappyout/example.078.AA.strNOG.ENOG411BH99.fasta
./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas/strict/example.078.AA.strNOG.ENOG411BH99.fasta
./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas/strictplus/example.078.AA.strNOG.ENOG411BH99.fasta
./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas/automated1/example.078.AA.strNOG.ENOG411BH99.fasta
./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas/nogaps/example.078.AA.strNOG.ENOG411BH99.fasta
./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas/noallgaps/example.078.AA.strNOG.ENOG411BH99.fasta
./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas/gappyout/example.079.AA.strNOG.ENOG411BJDC.fasta
./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas/strict/example.079.AA.strNOG.ENOG411BJDC.fasta
./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas/strictplus/example.079.AA.strNOG.ENOG411BJDC.fasta
./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas/automated1/example.079.AA.strNOG.ENOG411BJDC.fasta
./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas/nogaps/example.079.AA.strNOG.ENOG411BJDC.fasta
./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas/noallgaps/example.079.AA.strNOG.ENOG411BJDC.fasta
./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas/gappyout/example.080.AA.strNOG.ENOG411BJIF.fasta
./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas/strict/example.080.AA.strNOG.ENOG411BJIF.fasta
./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas/strictplus/example.080.AA.strNOG.ENOG411BJIF.fasta
./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas/automated1/example.080.AA.strNOG.ENOG411BJIF.fasta
./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas/nogaps/example.080.AA.strNOG.ENOG411BJIF.fasta
./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas/noallgaps/example.080.AA.strNOG.ENOG411BJIF.fasta
./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas/gappyout/example.081.AA.strNOG.ENOG411BK9X.fasta
./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas/strict/example.081.AA.strNOG.ENOG411BK9X.fasta
./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas/strictplus/example.081.AA.strNOG.ENOG411BK9X.fasta
./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas/automated1/example.081.AA.strNOG.ENOG411BK9X.fasta
./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas/nogaps/example.081.AA.strNOG.ENOG411BK9X.fasta
./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas/noallgaps/example.081.AA.strNOG.ENOG411BK9X.fasta
./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas/gappyout/example.082.AA.strNOG.ENOG411BKC5.fasta
./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas/strict/example.082.AA.strNOG.ENOG411BKC5.fasta
./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas/strictplus/example.082.AA.strNOG.ENOG411BKC5.fasta
./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas/automated1/example.082.AA.strNOG.ENOG411BKC5.fasta
./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas/nogaps/example.082.AA.strNOG.ENOG411BKC5.fasta
./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas/noallgaps/example.082.AA.strNOG.ENOG411BKC5.fasta
./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas/gappyout/example.083.AA.strNOG.ENOG411BMKC.fasta
./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas/strict/example.083.AA.strNOG.ENOG411BMKC.fasta
./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas/strictplus/example.083.AA.strNOG.ENOG411BMKC.fasta
./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas/automated1/example.083.AA.strNOG.ENOG411BMKC.fasta
./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas/nogaps/example.083.AA.strNOG.ENOG411BMKC.fasta
./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas/noallgaps/example.083.AA.strNOG.ENOG411BMKC.fasta
./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas/gappyout/example.084.AA.strNOG.ENOG411BNP9.fasta
./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas/strict/example.084.AA.strNOG.ENOG411BNP9.fasta
./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas/strictplus/example.084.AA.strNOG.ENOG411BNP9.fasta
./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas/automated1/example.084.AA.strNOG.ENOG411BNP9.fasta
./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas/nogaps/example.084.AA.strNOG.ENOG411BNP9.fasta
./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas/noallgaps/example.084.AA.strNOG.ENOG411BNP9.fasta
./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas/gappyout/example.085.AA.strNOG.ENOG411BQTJ.fasta
./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas/strict/example.085.AA.strNOG.ENOG411BQTJ.fasta
./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas/strictplus/example.085.AA.strNOG.ENOG411BQTJ.fasta
./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas/automated1/example.085.AA.strNOG.ENOG411BQTJ.fasta
./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas/nogaps/example.085.AA.strNOG.ENOG411BQTJ.fasta
./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas/noallgaps/example.085.AA.strNOG.ENOG411BQTJ.fasta
./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas/gappyout/example.086.AA.strNOG.ENOG411BR1D.fasta
./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas/strict/example.086.AA.strNOG.ENOG411BR1D.fasta
./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas/strictplus/example.086.AA.strNOG.ENOG411BR1D.fasta
./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas/automated1/example.086.AA.strNOG.ENOG411BR1D.fasta
./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas/nogaps/example.086.AA.strNOG.ENOG411BR1D.fasta
./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas/noallgaps/example.086.AA.strNOG.ENOG411BR1D.fasta
./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas/gappyout/example.087.AA.strNOG.ENOG411BRCH.fasta
./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas/strict/example.087.AA.strNOG.ENOG411BRCH.fasta
./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas/strictplus/example.087.AA.strNOG.ENOG411BRCH.fasta
./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas/automated1/example.087.AA.strNOG.ENOG411BRCH.fasta
./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas/nogaps/example.087.AA.strNOG.ENOG411BRCH.fasta
./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas/noallgaps/example.087.AA.strNOG.ENOG411BRCH.fasta
./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas/gappyout/example.088.AA.strNOG.ENOG411BSXF.fasta
./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas/strict/example.088.AA.strNOG.ENOG411BSXF.fasta
./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas/strictplus/example.088.AA.strNOG.ENOG411BSXF.fasta
./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas/automated1/example.088.AA.strNOG.ENOG411BSXF.fasta
./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas/nogaps/example.088.AA.strNOG.ENOG411BSXF.fasta
./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas/noallgaps/example.088.AA.strNOG.ENOG411BSXF.fasta
./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas/gappyout/example.089.AA.strNOG.ENOG411BV9B.fasta
./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas/strict/example.089.AA.strNOG.ENOG411BV9B.fasta
./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas/strictplus/example.089.AA.strNOG.ENOG411BV9B.fasta
./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas/automated1/example.089.AA.strNOG.ENOG411BV9B.fasta
./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas/nogaps/example.089.AA.strNOG.ENOG411BV9B.fasta
./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas/noallgaps/example.089.AA.strNOG.ENOG411BV9B.fasta
./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas/gappyout/example.090.AA.strNOG.ENOG411BVKR.fasta
./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas/strict/example.090.AA.strNOG.ENOG411BVKR.fasta
./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas/strictplus/example.090.AA.strNOG.ENOG411BVKR.fasta
./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas/automated1/example.090.AA.strNOG.ENOG411BVKR.fasta
./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas/nogaps/example.090.AA.strNOG.ENOG411BVKR.fasta
./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas/noallgaps/example.090.AA.strNOG.ENOG411BVKR.fasta
./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas/gappyout/example.091.AA.strNOG.ENOG411BWBU.fasta
./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas/strict/example.091.AA.strNOG.ENOG411BWBU.fasta
./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas/strictplus/example.091.AA.strNOG.ENOG411BWBU.fasta
./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas/automated1/example.091.AA.strNOG.ENOG411BWBU.fasta
./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas/nogaps/example.091.AA.strNOG.ENOG411BWBU.fasta
./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas/noallgaps/example.091.AA.strNOG.ENOG411BWBU.fasta
