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 5258 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 14.15% 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 ML estimate of 25 per site rate categories Likelihood of final tree will be evaluated and optimized under GAMMA GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units Partition: 0 Alignment Patterns: 5258 Name: No Name Provided DataType: AA Substitution Matrix: GTR Using empirical base frequencies RAxML was called as follows: raxml -f a -s supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov.fa -n RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov -m PROTCATGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 9051.064645 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2101.154039 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 327.253402 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 19.750284 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.794748 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Time for BS model parameter optimization 101.080778 Bootstrap[0]: Time 103.240673 seconds, bootstrap likelihood -90459.590765, best rearrangement setting 13 Bootstrap[1]: Time 4.498374 seconds, bootstrap likelihood -92108.837128, best rearrangement setting 13 Bootstrap[2]: Time 4.529753 seconds, bootstrap likelihood -91032.415765, best rearrangement setting 12 Bootstrap[3]: Time 1.795620 seconds, bootstrap likelihood -89606.385608, best rearrangement setting 15 Bootstrap[4]: Time 1.805840 seconds, bootstrap likelihood -89515.505698, best rearrangement setting 10 Bootstrap[5]: Time 1.792687 seconds, bootstrap likelihood -89507.020318, best rearrangement setting 10 Bootstrap[6]: Time 1.631986 seconds, bootstrap likelihood -90548.232925, best rearrangement setting 6 Bootstrap[7]: Time 4.466686 seconds, bootstrap likelihood -91337.227942, best rearrangement setting 14 Bootstrap[8]: Time 4.134083 seconds, bootstrap likelihood -90523.423609, best rearrangement setting 5 Bootstrap[9]: Time 4.160894 seconds, bootstrap likelihood -89496.536047, best rearrangement setting 7 Bootstrap[10]: Time 2.035553 seconds, bootstrap likelihood -90707.892302, best rearrangement setting 7 Bootstrap[11]: Time 1.703186 seconds, bootstrap likelihood -89380.840069, best rearrangement setting 5 Bootstrap[12]: Time 1.698341 seconds, bootstrap likelihood -90722.714583, best rearrangement setting 8 Bootstrap[13]: Time 1.767863 seconds, bootstrap likelihood -89341.916357, best rearrangement setting 7 Bootstrap[14]: Time 1.798201 seconds, bootstrap likelihood -90561.791285, best rearrangement setting 12 Bootstrap[15]: Time 1.930370 seconds, bootstrap likelihood -88716.839943, best rearrangement setting 15 Bootstrap[16]: Time 1.751366 seconds, bootstrap likelihood -90502.259538, best rearrangement setting 12 Bootstrap[17]: Time 4.359640 seconds, bootstrap likelihood -92261.540810, best rearrangement setting 12 Bootstrap[18]: Time 1.789822 seconds, bootstrap likelihood -89927.088581, best rearrangement setting 5 Bootstrap[19]: Time 4.501201 seconds, bootstrap likelihood -90548.154180, best rearrangement setting 8 Bootstrap[20]: Time 2.117485 seconds, bootstrap likelihood -91343.284861, best rearrangement setting 10 Bootstrap[21]: Time 1.795707 seconds, bootstrap likelihood -89965.477541, best rearrangement setting 6 Bootstrap[22]: Time 4.317523 seconds, bootstrap likelihood -90633.033167, best rearrangement setting 5 Bootstrap[23]: Time 4.639689 seconds, bootstrap likelihood -90701.875681, best rearrangement setting 7 Bootstrap[24]: Time 5.232994 seconds, bootstrap likelihood -89765.850741, best rearrangement setting 8 Bootstrap[25]: Time 4.025241 seconds, bootstrap likelihood -91352.391349, best rearrangement setting 6 Bootstrap[26]: Time 1.913374 seconds, bootstrap likelihood -90594.952648, best rearrangement setting 12 Bootstrap[27]: Time 4.164453 seconds, bootstrap likelihood -90051.910243, best rearrangement setting 10 Bootstrap[28]: Time 4.505897 seconds, bootstrap likelihood -89602.997694, best rearrangement setting 11 Bootstrap[29]: Time 4.370532 seconds, bootstrap likelihood -90614.934093, best rearrangement setting 12 Bootstrap[30]: Time 4.709495 seconds, bootstrap likelihood -90184.670527, best rearrangement setting 15 Bootstrap[31]: Time 4.742263 seconds, bootstrap likelihood -90683.934682, best rearrangement setting 15 Bootstrap[32]: Time 4.020706 seconds, bootstrap likelihood -89403.092782, best rearrangement setting 6 Bootstrap[33]: Time 4.400997 seconds, bootstrap likelihood -90834.915493, best rearrangement setting 15 Bootstrap[34]: Time 1.772876 seconds, bootstrap likelihood -90267.748045, best rearrangement setting 11 Bootstrap[35]: Time 1.707179 seconds, bootstrap likelihood -89754.460036, best rearrangement setting 8 Bootstrap[36]: Time 1.770945 seconds, bootstrap likelihood -90512.241177, best rearrangement setting 9 Bootstrap[37]: Time 1.759680 seconds, bootstrap likelihood -90613.484413, best rearrangement setting 11 Bootstrap[38]: Time 1.870121 seconds, bootstrap likelihood -90090.063204, best rearrangement setting 8 Bootstrap[39]: Time 1.738458 seconds, bootstrap likelihood -91428.267289, best rearrangement setting 13 Bootstrap[40]: Time 1.784474 seconds, bootstrap likelihood -89481.965563, best rearrangement setting 13 Bootstrap[41]: Time 1.750694 seconds, bootstrap likelihood -90297.187269, best rearrangement setting 10 Bootstrap[42]: Time 1.743567 seconds, bootstrap likelihood -91218.246092, best rearrangement setting 5 Bootstrap[43]: Time 1.783749 seconds, bootstrap likelihood -91868.512328, best rearrangement setting 14 Bootstrap[44]: Time 4.524497 seconds, bootstrap likelihood -91505.651809, best rearrangement setting 10 Bootstrap[45]: Time 1.690169 seconds, bootstrap likelihood -91022.127141, best rearrangement setting 15 Bootstrap[46]: Time 4.451747 seconds, bootstrap likelihood -90553.187215, best rearrangement setting 14 Bootstrap[47]: Time 1.759421 seconds, bootstrap likelihood -91522.931000, best rearrangement setting 8 Bootstrap[48]: Time 1.836844 seconds, bootstrap likelihood -89800.391774, best rearrangement setting 6 Bootstrap[49]: Time 1.839086 seconds, bootstrap likelihood -90357.202479, best rearrangement setting 7 Bootstrap[50]: Time 1.880770 seconds, bootstrap likelihood -90492.698654, best rearrangement setting 7 Bootstrap[51]: Time 4.631506 seconds, bootstrap likelihood -90625.344805, best rearrangement setting 11 Bootstrap[52]: Time 4.597045 seconds, bootstrap likelihood -90724.500900, best rearrangement setting 12 Bootstrap[53]: Time 4.103150 seconds, bootstrap likelihood -91382.239030, best rearrangement setting 8 Bootstrap[54]: Time 1.745416 seconds, bootstrap likelihood -90155.342933, best rearrangement setting 9 Bootstrap[55]: Time 1.636261 seconds, bootstrap likelihood -90581.733451, best rearrangement setting 11 Bootstrap[56]: Time 1.720914 seconds, bootstrap likelihood -91632.954357, best rearrangement setting 5 Bootstrap[57]: Time 1.668189 seconds, bootstrap likelihood -90067.550096, best rearrangement setting 7 Bootstrap[58]: Time 4.640681 seconds, bootstrap likelihood -89139.517305, best rearrangement setting 10 Bootstrap[59]: Time 4.425033 seconds, bootstrap likelihood -89314.510099, best rearrangement setting 9 Bootstrap[60]: Time 1.804177 seconds, bootstrap likelihood -89228.603977, best rearrangement setting 7 Bootstrap[61]: Time 1.774209 seconds, bootstrap likelihood -91020.069569, best rearrangement setting 5 Bootstrap[62]: Time 1.763344 seconds, bootstrap likelihood -90739.678870, best rearrangement setting 11 Bootstrap[63]: Time 4.448070 seconds, bootstrap likelihood -89795.089140, best rearrangement setting 12 Bootstrap[64]: Time 4.295241 seconds, bootstrap likelihood -90340.799365, best rearrangement setting 7 Bootstrap[65]: Time 4.486500 seconds, bootstrap likelihood -89495.410269, best rearrangement setting 5 Bootstrap[66]: Time 1.782376 seconds, bootstrap likelihood -91780.816260, best rearrangement setting 5 Bootstrap[67]: Time 1.822199 seconds, bootstrap likelihood -91719.867400, best rearrangement setting 15 Bootstrap[68]: Time 1.719228 seconds, bootstrap likelihood -91202.259416, best rearrangement setting 11 Bootstrap[69]: Time 4.139125 seconds, bootstrap likelihood -91570.345993, best rearrangement setting 5 Bootstrap[70]: Time 1.894140 seconds, bootstrap likelihood -90836.483865, best rearrangement setting 8 Bootstrap[71]: Time 1.743024 seconds, bootstrap likelihood -89720.434278, best rearrangement setting 10 Bootstrap[72]: Time 3.913624 seconds, bootstrap likelihood -90557.747112, best rearrangement setting 11 Bootstrap[73]: Time 1.707459 seconds, bootstrap likelihood -90704.037847, best rearrangement setting 9 Bootstrap[74]: Time 4.076349 seconds, bootstrap likelihood -91275.560405, best rearrangement setting 5 Bootstrap[75]: Time 4.405337 seconds, bootstrap likelihood -90614.702376, best rearrangement setting 8 Bootstrap[76]: Time 4.676458 seconds, bootstrap likelihood -89754.791219, best rearrangement setting 9 Bootstrap[77]: Time 1.764862 seconds, bootstrap likelihood -89529.822742, best rearrangement setting 11 Bootstrap[78]: Time 1.710131 seconds, bootstrap likelihood -90671.035882, best rearrangement setting 15 Bootstrap[79]: Time 1.709986 seconds, bootstrap likelihood -90616.765876, best rearrangement setting 9 Bootstrap[80]: Time 1.986625 seconds, bootstrap likelihood -92011.366148, best rearrangement setting 15 Bootstrap[81]: Time 4.204007 seconds, bootstrap likelihood -90817.256712, best rearrangement setting 7 Bootstrap[82]: Time 4.098841 seconds, bootstrap likelihood -90141.257531, best rearrangement setting 6 Bootstrap[83]: Time 1.680132 seconds, bootstrap likelihood -89697.149518, best rearrangement setting 10 Bootstrap[84]: Time 1.760331 seconds, bootstrap likelihood -90785.756247, best rearrangement setting 11 Bootstrap[85]: Time 1.783316 seconds, bootstrap likelihood -90845.908921, best rearrangement setting 8 Bootstrap[86]: Time 4.137192 seconds, bootstrap likelihood -90006.554027, best rearrangement setting 7 Bootstrap[87]: Time 1.602666 seconds, bootstrap likelihood -90699.439276, best rearrangement setting 7 Bootstrap[88]: Time 4.260047 seconds, bootstrap likelihood -89652.868200, best rearrangement setting 12 Bootstrap[89]: Time 1.697295 seconds, bootstrap likelihood -89758.234695, best rearrangement setting 10 Bootstrap[90]: Time 1.779878 seconds, bootstrap likelihood -90413.931910, best rearrangement setting 8 Bootstrap[91]: Time 1.650810 seconds, bootstrap likelihood -91011.982992, best rearrangement setting 12 Bootstrap[92]: Time 4.223809 seconds, bootstrap likelihood -90420.212887, best rearrangement setting 13 Bootstrap[93]: Time 3.916755 seconds, bootstrap likelihood -90564.539347, best rearrangement setting 15 Bootstrap[94]: Time 4.498961 seconds, bootstrap likelihood -91169.364470, best rearrangement setting 5 Bootstrap[95]: Time 4.528768 seconds, bootstrap likelihood -91363.031447, best rearrangement setting 5 Bootstrap[96]: Time 4.170893 seconds, bootstrap likelihood -89880.711086, best rearrangement setting 13 Bootstrap[97]: Time 4.690380 seconds, bootstrap likelihood -90632.512468, best rearrangement setting 11 Bootstrap[98]: Time 3.927132 seconds, bootstrap likelihood -91231.333644, best rearrangement setting 6 Bootstrap[99]: Time 4.641334 seconds, bootstrap likelihood -89606.448420, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 396.386584 seconds Average Time per Rapid Bootstrap 3.963866 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 1208.223662 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 49.313080 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 611.578940 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 48.600174 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.763111 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.143633 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.009706 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 382.027925 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1271.846502 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 51.455364 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 626.499016 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 65.048389 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.322427 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.184967 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.011595 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1353.221309 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 62.099569 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.927335 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.141304 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.015335 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -97644.866642 Slow ML Search 1 Likelihood: -97644.866643 Slow ML Search 2 Likelihood: -97644.866644 Slow ML Search 3 Likelihood: -97644.866645 Slow ML Search 4 Likelihood: -97644.866643 Slow ML Search 5 Likelihood: -97644.866642 Slow ML Search 6 Likelihood: -97644.866642 Slow ML Search 7 Likelihood: -97644.866642 Slow ML Search 8 Likelihood: -97644.866643 Slow ML Search 9 Likelihood: -97644.866646 Slow ML optimization finished Slow ML search Time: 540.028397 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1361.354677 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 62.713638 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.014359 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.147047 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.015857 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov_Partition_No Name Provided Thorough ML search Time: 308.310001 seconds Final ML Optimization Likelihood: -97639.275368 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.589973 Tree-Length: 5.470640 rate A <-> R: 0.464750 rate A <-> N: 0.696824 rate A <-> D: 1.898991 rate A <-> C: 3.546926 rate A <-> Q: 0.143826 rate A <-> E: 3.026774 rate A <-> G: 5.210175 rate A <-> H: 0.000000 rate A <-> I: 2.099645 rate A <-> L: 1.181579 rate A <-> K: 0.092170 rate A <-> M: 1.243582 rate A <-> F: 1.172621 rate A <-> P: 4.455928 rate A <-> S: 23.106724 rate A <-> T: 14.652777 rate A <-> W: 0.000000 rate A <-> Y: 0.000000 rate A <-> V: 13.475622 rate R <-> N: 0.266527 rate R <-> D: 0.000000 rate R <-> C: 0.496965 rate R <-> Q: 5.461186 rate R <-> E: 0.720918 rate R <-> G: 1.055565 rate R <-> H: 3.022971 rate R <-> I: 0.085184 rate R <-> L: 0.448583 rate R <-> K: 22.673904 rate R <-> M: 0.991694 rate R <-> F: 0.136471 rate R <-> P: 0.162319 rate R <-> S: 1.130770 rate R <-> T: 0.594618 rate R <-> W: 0.491585 rate R <-> Y: 0.219867 rate R <-> V: 0.000000 rate N <-> D: 15.096029 rate N <-> C: 0.966515 rate N <-> Q: 7.458994 rate N <-> E: 2.962189 rate N <-> G: 2.567018 rate N <-> H: 9.886648 rate N <-> I: 2.194315 rate N <-> L: 0.948391 rate N <-> K: 8.605278 rate N <-> M: 0.863144 rate N <-> F: 0.505384 rate N <-> P: 0.000000 rate N <-> S: 16.374580 rate N <-> T: 8.267990 rate N <-> W: 0.168980 rate N <-> Y: 3.752266 rate N <-> V: 0.471000 rate D <-> C: 0.970845 rate D <-> Q: 0.000000 rate D <-> E: 32.232469 rate D <-> G: 2.036991 rate D <-> H: 1.900411 rate D <-> I: 0.168278 rate D <-> L: 0.140904 rate D <-> K: 1.016954 rate D <-> M: 0.356501 rate D <-> F: 0.000000 rate D <-> P: 0.516323 rate D <-> S: 3.062311 rate D <-> T: 1.023237 rate D <-> W: 0.288383 rate D <-> Y: 0.844989 rate D <-> V: 0.138318 rate C <-> Q: 0.000000 rate C <-> E: 0.413330 rate C <-> G: 2.402795 rate C <-> H: 2.849048 rate C <-> I: 0.600194 rate C <-> L: 0.846868 rate C <-> K: 0.000000 rate C <-> M: 2.822374 rate C <-> F: 1.854208 rate C <-> P: 0.000000 rate C <-> S: 11.897027 rate C <-> T: 3.232993 rate C <-> W: 0.572536 rate C <-> Y: 4.111531 rate C <-> V: 4.933752 rate Q <-> E: 8.533792 rate Q <-> G: 0.000000 rate Q <-> H: 19.188548 rate Q <-> I: 0.511872 rate Q <-> L: 2.234187 rate Q <-> K: 6.461695 rate Q <-> M: 0.774424 rate Q <-> F: 0.000000 rate Q <-> P: 3.130982 rate Q <-> S: 1.343687 rate Q <-> T: 1.628658 rate Q <-> W: 0.033388 rate Q <-> Y: 2.135798 rate Q <-> V: 0.000000 rate E <-> G: 2.205877 rate E <-> H: 0.216571 rate E <-> I: 0.176289 rate E <-> L: 0.462928 rate E <-> K: 3.959849 rate E <-> M: 0.000000 rate E <-> F: 0.186899 rate E <-> P: 0.238437 rate E <-> S: 2.246379 rate E <-> T: 2.047045 rate E <-> W: 0.197735 rate E <-> Y: 0.959645 rate E <-> V: 0.432760 rate G <-> H: 0.731512 rate G <-> I: 0.151036 rate G <-> L: 0.032812 rate G <-> K: 0.357713 rate G <-> M: 0.134364 rate G <-> F: 0.299270 rate G <-> P: 0.000000 rate G <-> S: 6.151611 rate G <-> T: 0.273553 rate G <-> W: 0.579558 rate G <-> Y: 0.000000 rate G <-> V: 0.505169 rate H <-> I: 0.069916 rate H <-> L: 0.693539 rate H <-> K: 0.224993 rate H <-> M: 0.000000 rate H <-> F: 0.622293 rate H <-> P: 0.500529 rate H <-> S: 1.554803 rate H <-> T: 0.804532 rate H <-> W: 0.000000 rate H <-> Y: 11.902615 rate H <-> V: 0.000000 rate I <-> L: 17.565516 rate I <-> K: 1.203907 rate I <-> M: 16.170300 rate I <-> F: 3.401904 rate I <-> P: 0.194898 rate I <-> S: 0.897286 rate I <-> T: 8.857199 rate I <-> W: 0.357839 rate I <-> Y: 1.473115 rate I <-> V: 51.535220 rate L <-> K: 0.613600 rate L <-> M: 13.565879 rate L <-> F: 6.244960 rate L <-> P: 0.738269 rate L <-> S: 1.727233 rate L <-> T: 1.600273 rate L <-> W: 1.159693 rate L <-> Y: 1.104932 rate L <-> V: 4.206978 rate K <-> M: 0.746378 rate K <-> F: 0.078528 rate K <-> P: 0.369534 rate K <-> S: 1.830163 rate K <-> T: 2.075915 rate K <-> W: 0.147857 rate K <-> Y: 0.614304 rate K <-> V: 0.323466 rate M <-> F: 1.356100 rate M <-> P: 0.200436 rate M <-> S: 0.879749 rate M <-> T: 6.009322 rate M <-> W: 0.407518 rate M <-> Y: 0.398496 rate M <-> V: 7.540769 rate F <-> P: 0.209459 rate F <-> S: 1.378106 rate F <-> T: 0.634960 rate F <-> W: 0.847562 rate F <-> Y: 11.417619 rate F <-> V: 1.283253 rate P <-> S: 5.793766 rate P <-> T: 1.895523 rate P <-> W: 0.355555 rate P <-> Y: 0.720083 rate P <-> V: 0.694713 rate S <-> T: 23.641331 rate S <-> W: 0.349601 rate S <-> Y: 1.614694 rate S <-> V: 1.066704 rate T <-> W: 0.000000 rate T <-> Y: 1.496480 rate T <-> V: 11.693209 rate W <-> Y: 1.093122 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.042997 freq pi(R): 0.040701 freq pi(N): 0.062101 freq pi(D): 0.027824 freq pi(C): 0.013535 freq pi(Q): 0.017351 freq pi(E): 0.033768 freq pi(G): 0.041510 freq pi(H): 0.018282 freq pi(I): 0.076306 freq pi(L): 0.120095 freq pi(K): 0.082978 freq pi(M): 0.018358 freq pi(F): 0.133996 freq pi(P): 0.022554 freq pi(S): 0.073707 freq pi(T): 0.046814 freq pi(W): 0.016227 freq pi(Y): 0.053887 freq pi(V): 0.057008 ML search took 1230.787792 secs or 0.341885 hours Combined Bootstrap and ML search took 1627.178977 secs or 0.451994 hours Drawing Bootstrap Support Values on best-scoring ML tree ... Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bootstrap.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov Best-scoring ML tree written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov Best-scoring ML tree with support values written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitions.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov Best-scoring ML tree with support values as branch labels written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitionsBranchLabels.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov Overall execution time for full ML analysis: 1627.240267 secs or 0.452011 hours or 0.018834 days