IMPORTANT WARNING: Sequences P_tetraurelia-Sample_291_60aa-ORF_renamed_min100aa_ORF and P_tetraurelia-Sample_99_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_tetraurelia-Sample_291_60aa-ORF_renamed_min100aa_ORF and P_tetraurelia-Sample_A_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_biaurelia-Sample_379_60aa-ORF_renamed_min100aa_ORF and P_biaurelia-Sample_USBL-36I1_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_128_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_130_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_134_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_137_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_127_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_131_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences Tetrahymena_malaccensis and Tetrahymena_pigmentosa are exactly identical IMPORTANT WARNING Found 9 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. Just in case you might need it, an alignment file with sequence duplicates removed is printed to file Ymf57.renamed.muscle.Oligohymenophorea.fa.reduced This is RAxML version 8.1.3 released by Alexandros Stamatakis on August 13 2014. With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Alexey Kozlov (HITS) Kassian Kobert (HITS) David Dao (KIT and HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (NRIFS) Alignment has 93 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 14.55% RAxML rapid bootstrapping and subsequent ML search Using 1 distinct models/data partitions with joint branch length optimization Executing 100 rapid bootstrap inferences and thereafter a thorough ML search All free model parameters will be estimated by RAxML GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units Partition: 0 Alignment Patterns: 93 Name: No Name Provided DataType: AA Substitution Matrix: GTR Using empirical base frequencies RAxML was called as follows: 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 Printed linked AA GTR matrix that achieved an overall improvement of 76.144925 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 10.925666 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.532788 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Time for BS model parameter optimization 13.818215 Bootstrap[0]: Time 14.770109 seconds, bootstrap likelihood -1123.886188, best rearrangement setting 13 Bootstrap[1]: Time 0.931094 seconds, bootstrap likelihood -1204.033489, best rearrangement setting 13 Bootstrap[2]: Time 0.876496 seconds, bootstrap likelihood -1036.268494, best rearrangement setting 12 Bootstrap[3]: Time 0.793382 seconds, bootstrap likelihood -1069.098606, best rearrangement setting 15 Bootstrap[4]: Time 0.939990 seconds, bootstrap likelihood -1187.036970, best rearrangement setting 10 Bootstrap[5]: Time 0.733979 seconds, bootstrap likelihood -1090.230789, best rearrangement setting 10 Bootstrap[6]: Time 0.867288 seconds, bootstrap likelihood -1152.711779, best rearrangement setting 6 Bootstrap[7]: Time 0.918969 seconds, bootstrap likelihood -1119.746720, best rearrangement setting 14 Bootstrap[8]: Time 0.696023 seconds, bootstrap likelihood -1214.831981, best rearrangement setting 5 Bootstrap[9]: Time 0.815712 seconds, bootstrap likelihood -1155.822001, best rearrangement setting 7 Bootstrap[10]: Time 1.099725 seconds, bootstrap likelihood -1023.469912, best rearrangement setting 7 Bootstrap[11]: Time 0.751532 seconds, bootstrap likelihood -1161.308319, best rearrangement setting 5 Bootstrap[12]: Time 0.798793 seconds, bootstrap likelihood -1182.953761, best rearrangement setting 8 Bootstrap[13]: Time 0.837813 seconds, bootstrap likelihood -1103.249666, best rearrangement setting 7 Bootstrap[14]: Time 0.755771 seconds, bootstrap likelihood -1142.611558, best rearrangement setting 12 Bootstrap[15]: Time 0.834500 seconds, bootstrap likelihood -1104.992341, best rearrangement setting 15 Bootstrap[16]: Time 0.718963 seconds, bootstrap likelihood -1121.237901, best rearrangement setting 12 Bootstrap[17]: Time 0.702593 seconds, bootstrap likelihood -1109.594350, best rearrangement setting 12 Bootstrap[18]: Time 0.783266 seconds, bootstrap likelihood -1024.142004, best rearrangement setting 5 Bootstrap[19]: Time 0.875388 seconds, bootstrap likelihood -1278.390621, best rearrangement setting 8 Bootstrap[20]: Time 0.760791 seconds, bootstrap likelihood -1157.183889, best rearrangement setting 10 Bootstrap[21]: Time 0.696321 seconds, bootstrap likelihood -1105.393625, best rearrangement setting 6 Bootstrap[22]: Time 0.707581 seconds, bootstrap likelihood -982.850630, best rearrangement setting 5 Bootstrap[23]: Time 0.773908 seconds, bootstrap likelihood -1139.109693, best rearrangement setting 7 Bootstrap[24]: Time 0.944539 seconds, bootstrap likelihood -1166.559479, best rearrangement setting 8 Bootstrap[25]: Time 0.833182 seconds, bootstrap likelihood -1102.061994, best rearrangement setting 6 Bootstrap[26]: Time 0.890487 seconds, bootstrap likelihood -1029.374834, best rearrangement setting 12 Bootstrap[27]: Time 0.784878 seconds, bootstrap likelihood -1107.898404, best rearrangement setting 10 Bootstrap[28]: Time 0.887994 seconds, bootstrap likelihood -1128.842063, best rearrangement setting 11 Bootstrap[29]: Time 1.034663 seconds, bootstrap likelihood -1117.343840, best rearrangement setting 12 Bootstrap[30]: Time 0.745518 seconds, bootstrap likelihood -1133.715486, best rearrangement setting 15 Bootstrap[31]: Time 0.976341 seconds, bootstrap likelihood -1187.628564, best rearrangement setting 15 Bootstrap[32]: Time 0.985588 seconds, bootstrap likelihood -1119.958019, best rearrangement setting 6 Bootstrap[33]: Time 0.875409 seconds, bootstrap likelihood -1173.813874, best rearrangement setting 15 Bootstrap[34]: Time 0.834846 seconds, bootstrap likelihood -1088.258765, best rearrangement setting 11 Bootstrap[35]: Time 0.720924 seconds, bootstrap likelihood -1094.431799, best rearrangement setting 8 Bootstrap[36]: Time 0.683909 seconds, bootstrap likelihood -1022.173852, best rearrangement setting 9 Bootstrap[37]: Time 0.712563 seconds, bootstrap likelihood -1188.426343, best rearrangement setting 11 Bootstrap[38]: Time 0.928828 seconds, bootstrap likelihood -1096.482748, best rearrangement setting 8 Bootstrap[39]: Time 0.949406 seconds, bootstrap likelihood -1131.222367, best rearrangement setting 13 Bootstrap[40]: Time 0.844910 seconds, bootstrap likelihood -1133.799904, best rearrangement setting 13 Bootstrap[41]: Time 0.906585 seconds, bootstrap likelihood -1158.245593, best rearrangement setting 10 Bootstrap[42]: Time 0.964017 seconds, bootstrap likelihood -1111.179108, best rearrangement setting 5 Bootstrap[43]: Time 1.137873 seconds, bootstrap likelihood -1089.412864, best rearrangement setting 14 Bootstrap[44]: Time 0.895204 seconds, bootstrap likelihood -1034.584398, best rearrangement setting 10 Bootstrap[45]: Time 0.942406 seconds, bootstrap likelihood -1055.800116, best rearrangement setting 15 Bootstrap[46]: Time 1.063261 seconds, bootstrap likelihood -1028.480099, best rearrangement setting 14 Bootstrap[47]: Time 0.835071 seconds, bootstrap likelihood -1055.548474, best rearrangement setting 8 Bootstrap[48]: Time 0.934722 seconds, bootstrap likelihood -1148.237434, best rearrangement setting 6 Bootstrap[49]: Time 0.894075 seconds, bootstrap likelihood -1212.421889, best rearrangement setting 7 Bootstrap[50]: Time 0.710799 seconds, bootstrap likelihood -1078.457908, best rearrangement setting 7 Bootstrap[51]: Time 0.817623 seconds, bootstrap likelihood -1204.187045, best rearrangement setting 11 Bootstrap[52]: Time 1.006294 seconds, bootstrap likelihood -1210.426370, best rearrangement setting 12 Bootstrap[53]: Time 0.708604 seconds, bootstrap likelihood -1137.768843, best rearrangement setting 8 Bootstrap[54]: Time 0.741993 seconds, bootstrap likelihood -1001.819137, best rearrangement setting 9 Bootstrap[55]: Time 0.746953 seconds, bootstrap likelihood -1238.183387, best rearrangement setting 11 Bootstrap[56]: Time 0.842999 seconds, bootstrap likelihood -1225.222649, best rearrangement setting 5 Bootstrap[57]: Time 1.100984 seconds, bootstrap likelihood -1132.553797, best rearrangement setting 7 Bootstrap[58]: Time 0.878347 seconds, bootstrap likelihood -1191.089402, best rearrangement setting 10 Bootstrap[59]: Time 0.768264 seconds, bootstrap likelihood -1113.379456, best rearrangement setting 9 Bootstrap[60]: Time 0.812010 seconds, bootstrap likelihood -1104.095219, best rearrangement setting 7 Bootstrap[61]: Time 0.617217 seconds, bootstrap likelihood -1099.429946, best rearrangement setting 5 Bootstrap[62]: Time 0.654992 seconds, bootstrap likelihood -1089.435622, best rearrangement setting 11 Bootstrap[63]: Time 0.677902 seconds, bootstrap likelihood -967.098585, best rearrangement setting 12 Bootstrap[64]: Time 0.716789 seconds, bootstrap likelihood -1195.867046, best rearrangement setting 7 Bootstrap[65]: Time 0.819465 seconds, bootstrap likelihood -1111.917390, best rearrangement setting 5 Bootstrap[66]: Time 0.916864 seconds, bootstrap likelihood -1193.740231, best rearrangement setting 5 Bootstrap[67]: Time 0.761630 seconds, bootstrap likelihood -992.126329, best rearrangement setting 15 Bootstrap[68]: Time 0.715562 seconds, bootstrap likelihood -1106.080441, best rearrangement setting 11 Bootstrap[69]: Time 0.712955 seconds, bootstrap likelihood -1097.586218, best rearrangement setting 5 Bootstrap[70]: Time 0.815720 seconds, bootstrap likelihood -1034.231237, best rearrangement setting 8 Bootstrap[71]: Time 0.868905 seconds, bootstrap likelihood -1141.589272, best rearrangement setting 10 Bootstrap[72]: Time 0.779052 seconds, bootstrap likelihood -1263.025824, best rearrangement setting 11 Bootstrap[73]: Time 0.722529 seconds, bootstrap likelihood -1077.829405, best rearrangement setting 9 Bootstrap[74]: Time 0.758640 seconds, bootstrap likelihood -1195.929393, best rearrangement setting 5 Bootstrap[75]: Time 0.835765 seconds, bootstrap likelihood -1141.450493, best rearrangement setting 8 Bootstrap[76]: Time 0.851401 seconds, bootstrap likelihood -1043.530579, best rearrangement setting 9 Bootstrap[77]: Time 0.927139 seconds, bootstrap likelihood -1065.147797, best rearrangement setting 11 Bootstrap[78]: Time 0.787801 seconds, bootstrap likelihood -1172.855873, best rearrangement setting 15 Bootstrap[79]: Time 0.891673 seconds, bootstrap likelihood -1089.075812, best rearrangement setting 9 Bootstrap[80]: Time 0.853914 seconds, bootstrap likelihood -1107.664839, best rearrangement setting 15 Bootstrap[81]: Time 0.724351 seconds, bootstrap likelihood -1055.114662, best rearrangement setting 7 Bootstrap[82]: Time 0.871573 seconds, bootstrap likelihood -1173.304136, best rearrangement setting 6 Bootstrap[83]: Time 0.771190 seconds, bootstrap likelihood -1158.181126, best rearrangement setting 10 Bootstrap[84]: Time 0.929493 seconds, bootstrap likelihood -1084.400119, best rearrangement setting 11 Bootstrap[85]: Time 0.841749 seconds, bootstrap likelihood -1236.136972, best rearrangement setting 8 Bootstrap[86]: Time 0.290373 seconds, bootstrap likelihood -1132.543836, best rearrangement setting 7 Bootstrap[87]: Time 1.027542 seconds, bootstrap likelihood -1015.778171, best rearrangement setting 7 Bootstrap[88]: Time 0.817908 seconds, bootstrap likelihood -1152.045924, best rearrangement setting 12 Bootstrap[89]: Time 0.993247 seconds, bootstrap likelihood -1162.252936, best rearrangement setting 10 Bootstrap[90]: Time 0.750157 seconds, bootstrap likelihood -1058.547272, best rearrangement setting 8 Bootstrap[91]: Time 0.717867 seconds, bootstrap likelihood -1306.593785, best rearrangement setting 12 Bootstrap[92]: Time 0.752374 seconds, bootstrap likelihood -1208.236388, best rearrangement setting 13 Bootstrap[93]: Time 0.786088 seconds, bootstrap likelihood -1035.139425, best rearrangement setting 15 Bootstrap[94]: Time 0.896756 seconds, bootstrap likelihood -1161.907466, best rearrangement setting 5 Bootstrap[95]: Time 0.784063 seconds, bootstrap likelihood -1084.136087, best rearrangement setting 5 Bootstrap[96]: Time 0.745851 seconds, bootstrap likelihood -1081.957662, best rearrangement setting 13 Bootstrap[97]: Time 0.772313 seconds, bootstrap likelihood -1124.571182, best rearrangement setting 11 Bootstrap[98]: Time 0.796726 seconds, bootstrap likelihood -1017.680379, best rearrangement setting 6 Bootstrap[99]: Time 0.930261 seconds, bootstrap likelihood -1082.621199, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 96.777791 seconds Average Time per Rapid Bootstrap 0.967778 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 73.127894 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 9.463237 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.401299 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.372641 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.007221 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 60.671061 seconds Printed linked AA GTR matrix that achieved an overall improvement of 74.660456 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 11.206266 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.579355 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.213939 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.004501 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf57.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Slow ML Search 0 Likelihood: -1150.116571 Slow ML Search 1 Likelihood: -1150.116571 Slow ML Search 2 Likelihood: -1150.116571 Slow ML Search 3 Likelihood: -1150.116571 Slow ML Search 4 Likelihood: -1150.116571 Slow ML Search 5 Likelihood: -1150.116571 Slow ML Search 6 Likelihood: -1150.116573 Slow ML Search 7 Likelihood: -1150.116573 Slow ML Search 8 Likelihood: -1150.116591 Slow ML Search 9 Likelihood: -1150.206199 Slow ML optimization finished Slow ML search Time: 48.678172 seconds