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 6301 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 13.11% 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: 6301 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.95perc_cov.fa -n RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov -m PROTCATGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 10690.831093 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1674.143811 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 451.216967 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 30.092149 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.992824 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.95perc_cov_Partition_No Name Provided Time for BS model parameter optimization 118.629048 Bootstrap[0]: Time 121.022718 seconds, bootstrap likelihood -108864.276038, best rearrangement setting 13 Bootstrap[1]: Time 1.965204 seconds, bootstrap likelihood -108639.930075, best rearrangement setting 13 Bootstrap[2]: Time 1.989180 seconds, bootstrap likelihood -109007.885659, best rearrangement setting 12 Bootstrap[3]: Time 4.385868 seconds, bootstrap likelihood -107700.647463, best rearrangement setting 15 Bootstrap[4]: Time 1.896084 seconds, bootstrap likelihood -110041.771221, best rearrangement setting 10 Bootstrap[5]: Time 4.752438 seconds, bootstrap likelihood -108774.018942, best rearrangement setting 10 Bootstrap[6]: Time 1.921294 seconds, bootstrap likelihood -108384.495134, best rearrangement setting 6 Bootstrap[7]: Time 5.069595 seconds, bootstrap likelihood -109979.837409, best rearrangement setting 14 Bootstrap[8]: Time 4.782530 seconds, bootstrap likelihood -109984.726835, best rearrangement setting 5 Bootstrap[9]: Time 4.740932 seconds, bootstrap likelihood -107875.215945, best rearrangement setting 7 Bootstrap[10]: Time 2.146305 seconds, bootstrap likelihood -109903.760038, best rearrangement setting 7 Bootstrap[11]: Time 4.645301 seconds, bootstrap likelihood -108260.867547, best rearrangement setting 5 Bootstrap[12]: Time 4.736856 seconds, bootstrap likelihood -108300.589372, best rearrangement setting 8 Bootstrap[13]: Time 4.503694 seconds, bootstrap likelihood -108755.651254, best rearrangement setting 7 Bootstrap[14]: Time 4.477614 seconds, bootstrap likelihood -109184.626254, best rearrangement setting 12 Bootstrap[15]: Time 2.169462 seconds, bootstrap likelihood -109990.456091, best rearrangement setting 15 Bootstrap[16]: Time 2.032501 seconds, bootstrap likelihood -108349.333713, best rearrangement setting 12 Bootstrap[17]: Time 2.057967 seconds, bootstrap likelihood -109223.117912, best rearrangement setting 12 Bootstrap[18]: Time 4.513277 seconds, bootstrap likelihood -108240.542113, best rearrangement setting 5 Bootstrap[19]: Time 4.850735 seconds, bootstrap likelihood -109248.164912, best rearrangement setting 8 Bootstrap[20]: Time 5.296266 seconds, bootstrap likelihood -108166.838481, best rearrangement setting 10 Bootstrap[21]: Time 4.959436 seconds, bootstrap likelihood -108912.249718, best rearrangement setting 6 Bootstrap[22]: Time 1.859615 seconds, bootstrap likelihood -107415.491945, best rearrangement setting 5 Bootstrap[23]: Time 5.141481 seconds, bootstrap likelihood -108987.435350, best rearrangement setting 7 Bootstrap[24]: Time 5.395315 seconds, bootstrap likelihood -109052.687975, best rearrangement setting 8 Bootstrap[25]: Time 2.004376 seconds, bootstrap likelihood -108703.820745, best rearrangement setting 6 Bootstrap[26]: Time 4.915177 seconds, bootstrap likelihood -108693.461595, best rearrangement setting 12 Bootstrap[27]: Time 4.610331 seconds, bootstrap likelihood -107012.043199, best rearrangement setting 10 Bootstrap[28]: Time 1.905888 seconds, bootstrap likelihood -109322.370662, best rearrangement setting 11 Bootstrap[29]: Time 4.716486 seconds, bootstrap likelihood -107939.648893, best rearrangement setting 12 Bootstrap[30]: Time 2.040786 seconds, bootstrap likelihood -108436.290331, best rearrangement setting 15 Bootstrap[31]: Time 4.756588 seconds, bootstrap likelihood -109555.591852, best rearrangement setting 15 Bootstrap[32]: Time 4.768397 seconds, bootstrap likelihood -109691.976948, best rearrangement setting 6 Bootstrap[33]: Time 4.489073 seconds, bootstrap likelihood -109908.350723, best rearrangement setting 15 Bootstrap[34]: Time 4.853721 seconds, bootstrap likelihood -109904.075138, best rearrangement setting 11 Bootstrap[35]: Time 2.102339 seconds, bootstrap likelihood -108128.849929, best rearrangement setting 8 Bootstrap[36]: Time 1.978275 seconds, bootstrap likelihood -109566.962565, best rearrangement setting 9 Bootstrap[37]: Time 5.195354 seconds, bootstrap likelihood -108660.970629, best rearrangement setting 11 Bootstrap[38]: Time 4.983601 seconds, bootstrap likelihood -109030.370277, best rearrangement setting 8 Bootstrap[39]: Time 1.977175 seconds, bootstrap likelihood -107429.102367, best rearrangement setting 13 Bootstrap[40]: Time 2.094113 seconds, bootstrap likelihood -110124.657789, best rearrangement setting 13 Bootstrap[41]: Time 1.933292 seconds, bootstrap likelihood -109748.278698, best rearrangement setting 10 Bootstrap[42]: Time 1.873261 seconds, bootstrap likelihood -109411.866277, best rearrangement setting 5 Bootstrap[43]: Time 1.865752 seconds, bootstrap likelihood -107767.815534, best rearrangement setting 14 Bootstrap[44]: Time 2.052165 seconds, bootstrap likelihood -109052.674449, best rearrangement setting 10 Bootstrap[45]: Time 4.446239 seconds, bootstrap likelihood -108995.133384, best rearrangement setting 15 Bootstrap[46]: Time 4.800770 seconds, bootstrap likelihood -109414.179262, best rearrangement setting 14 Bootstrap[47]: Time 4.814690 seconds, bootstrap likelihood -109396.204572, best rearrangement setting 8 Bootstrap[48]: Time 4.778710 seconds, bootstrap likelihood -110025.514273, best rearrangement setting 6 Bootstrap[49]: Time 4.605406 seconds, bootstrap likelihood -109968.957270, best rearrangement setting 7 Bootstrap[50]: Time 2.158677 seconds, bootstrap likelihood -109027.054049, best rearrangement setting 7 Bootstrap[51]: Time 1.873637 seconds, bootstrap likelihood -107679.477238, best rearrangement setting 11 Bootstrap[52]: Time 2.056773 seconds, bootstrap likelihood -109347.899455, best rearrangement setting 12 Bootstrap[53]: Time 1.979170 seconds, bootstrap likelihood -109580.410098, best rearrangement setting 8 Bootstrap[54]: Time 1.853284 seconds, bootstrap likelihood -108925.296686, best rearrangement setting 9 Bootstrap[55]: Time 2.049888 seconds, bootstrap likelihood -108950.767306, best rearrangement setting 11 Bootstrap[56]: Time 2.041510 seconds, bootstrap likelihood -107322.378097, best rearrangement setting 5 Bootstrap[57]: Time 5.259507 seconds, bootstrap likelihood -108448.525340, best rearrangement setting 7 Bootstrap[58]: Time 5.155530 seconds, bootstrap likelihood -111070.728170, best rearrangement setting 10 Bootstrap[59]: Time 2.095751 seconds, bootstrap likelihood -109380.607089, best rearrangement setting 9 Bootstrap[60]: Time 4.792553 seconds, bootstrap likelihood -109350.901612, best rearrangement setting 7 Bootstrap[61]: Time 4.648102 seconds, bootstrap likelihood -109149.446709, best rearrangement setting 5 Bootstrap[62]: Time 4.619311 seconds, bootstrap likelihood -108741.093564, best rearrangement setting 11 Bootstrap[63]: Time 4.724716 seconds, bootstrap likelihood -108132.191058, best rearrangement setting 12 Bootstrap[64]: Time 4.719515 seconds, bootstrap likelihood -109080.069376, best rearrangement setting 7 Bootstrap[65]: Time 4.635622 seconds, bootstrap likelihood -109928.343051, best rearrangement setting 5 Bootstrap[66]: Time 5.189801 seconds, bootstrap likelihood -109814.183618, best rearrangement setting 5 Bootstrap[67]: Time 5.083873 seconds, bootstrap likelihood -109027.526216, best rearrangement setting 15 Bootstrap[68]: Time 4.659399 seconds, bootstrap likelihood -108234.369195, best rearrangement setting 11 Bootstrap[69]: Time 4.546624 seconds, bootstrap likelihood -109048.266865, best rearrangement setting 5 Bootstrap[70]: Time 2.163099 seconds, bootstrap likelihood -108699.079352, best rearrangement setting 8 Bootstrap[71]: Time 4.595976 seconds, bootstrap likelihood -109109.619295, best rearrangement setting 10 Bootstrap[72]: Time 4.749473 seconds, bootstrap likelihood -108567.532437, best rearrangement setting 11 Bootstrap[73]: Time 1.991517 seconds, bootstrap likelihood -108919.090038, best rearrangement setting 9 Bootstrap[74]: Time 4.699469 seconds, bootstrap likelihood -108794.859761, best rearrangement setting 5 Bootstrap[75]: Time 2.127713 seconds, bootstrap likelihood -108908.338362, best rearrangement setting 8 Bootstrap[76]: Time 4.858599 seconds, bootstrap likelihood -108922.821195, best rearrangement setting 9 Bootstrap[77]: Time 5.380289 seconds, bootstrap likelihood -109341.896777, best rearrangement setting 11 Bootstrap[78]: Time 5.189859 seconds, bootstrap likelihood -108985.864378, best rearrangement setting 15 Bootstrap[79]: Time 4.713989 seconds, bootstrap likelihood -109174.437803, best rearrangement setting 9 Bootstrap[80]: Time 4.709985 seconds, bootstrap likelihood -109048.399805, best rearrangement setting 15 Bootstrap[81]: Time 4.737809 seconds, bootstrap likelihood -107778.944440, best rearrangement setting 7 Bootstrap[82]: Time 1.867894 seconds, bootstrap likelihood -107796.808654, best rearrangement setting 6 Bootstrap[83]: Time 4.904663 seconds, bootstrap likelihood -108883.901557, best rearrangement setting 10 Bootstrap[84]: Time 4.804155 seconds, bootstrap likelihood -109220.473481, best rearrangement setting 11 Bootstrap[85]: Time 2.036213 seconds, bootstrap likelihood -109150.803452, best rearrangement setting 8 Bootstrap[86]: Time 1.834279 seconds, bootstrap likelihood -108343.310665, best rearrangement setting 7 Bootstrap[87]: Time 4.575136 seconds, bootstrap likelihood -108187.667534, best rearrangement setting 7 Bootstrap[88]: Time 4.673269 seconds, bootstrap likelihood -108393.417759, best rearrangement setting 12 Bootstrap[89]: Time 4.490471 seconds, bootstrap likelihood -108556.782987, best rearrangement setting 10 Bootstrap[90]: Time 2.107022 seconds, bootstrap likelihood -108993.153128, best rearrangement setting 8 Bootstrap[91]: Time 2.136256 seconds, bootstrap likelihood -110114.131928, best rearrangement setting 12 Bootstrap[92]: Time 1.933656 seconds, bootstrap likelihood -109871.772702, best rearrangement setting 13 Bootstrap[93]: Time 2.012111 seconds, bootstrap likelihood -107384.691986, best rearrangement setting 15 Bootstrap[94]: Time 4.372498 seconds, bootstrap likelihood -109394.417674, best rearrangement setting 5 Bootstrap[95]: Time 4.663652 seconds, bootstrap likelihood -108611.075883, best rearrangement setting 5 Bootstrap[96]: Time 4.638487 seconds, bootstrap likelihood -109330.258193, best rearrangement setting 13 Bootstrap[97]: Time 4.801168 seconds, bootstrap likelihood -110119.225764, best rearrangement setting 11 Bootstrap[98]: Time 4.610503 seconds, bootstrap likelihood -108089.414432, best rearrangement setting 6 Bootstrap[99]: Time 4.659364 seconds, bootstrap likelihood -110046.407777, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 489.452872 seconds Average Time per Rapid Bootstrap 4.894529 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 2042.203966 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 131.543462 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 7.779498 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.340060 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.018097 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.95perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 418.507303 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1427.482213 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 51.329890 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.036677 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.079415 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1570.904921 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 67.406816 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.036905 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.129072 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.014600 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.95perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -116561.727227 Slow ML Search 1 Likelihood: -116561.727226 Slow ML Search 2 Likelihood: -116561.727227 Slow ML Search 3 Likelihood: -116561.727226 Slow ML Search 4 Likelihood: -116561.727226 Slow ML Search 5 Likelihood: -116561.727228 Slow ML Search 6 Likelihood: -116561.727225 Slow ML Search 7 Likelihood: -116561.727226 Slow ML Search 8 Likelihood: -116561.727226 Slow ML Search 9 Likelihood: -116561.727228 Slow ML optimization finished Slow ML search Time: 563.945290 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1570.713317 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 67.168355 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.029379 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.130609 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.014900 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.95perc_cov_Partition_No Name Provided Thorough ML search Time: 363.182365 seconds Final ML Optimization Likelihood: -116561.731520 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.611170 Tree-Length: 5.496979 rate A <-> R: 0.373999 rate A <-> N: 0.717580 rate A <-> D: 1.836428 rate A <-> C: 3.902402 rate A <-> Q: 0.202044 rate A <-> E: 2.815369 rate A <-> G: 4.908623 rate A <-> H: 0.066074 rate A <-> I: 1.961173 rate A <-> L: 1.204156 rate A <-> K: 0.159592 rate A <-> M: 0.886327 rate A <-> F: 1.181429 rate A <-> P: 4.352398 rate A <-> S: 23.245646 rate A <-> T: 14.087276 rate A <-> W: 0.000000 rate A <-> Y: 0.059371 rate A <-> V: 13.884662 rate R <-> N: 0.391912 rate R <-> D: 0.000000 rate R <-> C: 0.746626 rate R <-> Q: 5.581961 rate R <-> E: 0.762113 rate R <-> G: 1.099267 rate R <-> H: 3.125016 rate R <-> I: 0.228645 rate R <-> L: 0.430497 rate R <-> K: 23.698694 rate R <-> M: 0.959609 rate R <-> F: 0.193788 rate R <-> P: 0.237236 rate R <-> S: 1.219850 rate R <-> T: 0.540739 rate R <-> W: 0.698429 rate R <-> Y: 0.215228 rate R <-> V: 0.000000 rate N <-> D: 15.283394 rate N <-> C: 1.043882 rate N <-> Q: 7.500030 rate N <-> E: 3.339241 rate N <-> G: 2.530706 rate N <-> H: 9.543866 rate N <-> I: 2.084795 rate N <-> L: 0.839741 rate N <-> K: 8.647860 rate N <-> M: 0.879055 rate N <-> F: 0.433254 rate N <-> P: 0.369421 rate N <-> S: 16.032297 rate N <-> T: 8.943944 rate N <-> W: 0.260045 rate N <-> Y: 3.554444 rate N <-> V: 0.476606 rate D <-> C: 0.761291 rate D <-> Q: 0.000000 rate D <-> E: 32.241071 rate D <-> G: 2.362359 rate D <-> H: 1.708462 rate D <-> I: 0.154043 rate D <-> L: 0.162239 rate D <-> K: 0.940745 rate D <-> M: 0.057956 rate D <-> F: 0.064830 rate D <-> P: 0.674316 rate D <-> S: 3.068935 rate D <-> T: 1.357233 rate D <-> W: 0.244640 rate D <-> Y: 0.722333 rate D <-> V: 0.309318 rate C <-> Q: 0.000000 rate C <-> E: 0.274806 rate C <-> G: 2.978421 rate C <-> H: 2.596832 rate C <-> I: 0.814993 rate C <-> L: 1.432452 rate C <-> K: 0.000000 rate C <-> M: 1.900693 rate C <-> F: 1.865007 rate C <-> P: 0.000000 rate C <-> S: 11.414022 rate C <-> T: 2.880213 rate C <-> W: 0.507248 rate C <-> Y: 3.947581 rate C <-> V: 4.548162 rate Q <-> E: 7.902561 rate Q <-> G: 0.000000 rate Q <-> H: 20.558263 rate Q <-> I: 0.379984 rate Q <-> L: 1.727666 rate Q <-> K: 6.290969 rate Q <-> M: 0.930767 rate Q <-> F: 0.227411 rate Q <-> P: 3.061234 rate Q <-> S: 1.890821 rate Q <-> T: 1.654618 rate Q <-> W: 0.000000 rate Q <-> Y: 1.498625 rate Q <-> V: 0.000000 rate E <-> G: 2.194044 rate E <-> H: 0.139506 rate E <-> I: 0.181351 rate E <-> L: 0.444467 rate E <-> K: 4.054270 rate E <-> M: 0.000000 rate E <-> F: 0.195876 rate E <-> P: 0.194148 rate E <-> S: 2.372052 rate E <-> T: 1.722785 rate E <-> W: 0.201236 rate E <-> Y: 0.824674 rate E <-> V: 0.554239 rate G <-> H: 0.746491 rate G <-> I: 0.125325 rate G <-> L: 0.032144 rate G <-> K: 0.299225 rate G <-> M: 0.112920 rate G <-> F: 0.259596 rate G <-> P: 0.124744 rate G <-> S: 6.074208 rate G <-> T: 0.205689 rate G <-> W: 0.649368 rate G <-> Y: 0.000000 rate G <-> V: 0.542899 rate H <-> I: 0.099122 rate H <-> L: 0.888172 rate H <-> K: 0.266906 rate H <-> M: 0.000000 rate H <-> F: 0.711407 rate H <-> P: 0.348756 rate H <-> S: 1.731429 rate H <-> T: 1.412356 rate H <-> W: 0.000000 rate H <-> Y: 11.911830 rate H <-> V: 0.000000 rate I <-> L: 17.517432 rate I <-> K: 1.187556 rate I <-> M: 15.927834 rate I <-> F: 3.154284 rate I <-> P: 0.104368 rate I <-> S: 1.048994 rate I <-> T: 8.471075 rate I <-> W: 0.470733 rate I <-> Y: 1.757751 rate I <-> V: 51.669185 rate L <-> K: 0.656519 rate L <-> M: 13.056949 rate L <-> F: 6.217686 rate L <-> P: 0.992727 rate L <-> S: 1.755187 rate L <-> T: 1.595901 rate L <-> W: 1.303164 rate L <-> Y: 1.124789 rate L <-> V: 4.539575 rate K <-> M: 0.678542 rate K <-> F: 0.111128 rate K <-> P: 0.375001 rate K <-> S: 1.979165 rate K <-> T: 1.805437 rate K <-> W: 0.174639 rate K <-> Y: 0.640690 rate K <-> V: 0.261784 rate M <-> F: 1.274265 rate M <-> P: 0.196083 rate M <-> S: 0.718192 rate M <-> T: 5.630085 rate M <-> W: 0.381759 rate M <-> Y: 0.303116 rate M <-> V: 6.967745 rate F <-> P: 0.202383 rate F <-> S: 1.294106 rate F <-> T: 0.595467 rate F <-> W: 0.933463 rate F <-> Y: 10.667614 rate F <-> V: 1.305531 rate P <-> S: 5.716754 rate P <-> T: 3.031223 rate P <-> W: 0.543739 rate P <-> Y: 0.696233 rate P <-> V: 0.690753 rate S <-> T: 22.932808 rate S <-> W: 0.289271 rate S <-> Y: 1.449523 rate S <-> V: 1.289268 rate T <-> W: 0.000000 rate T <-> Y: 1.165934 rate T <-> V: 11.934318 rate W <-> Y: 1.555796 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.043508 freq pi(R): 0.038292 freq pi(N): 0.062483 freq pi(D): 0.027575 freq pi(C): 0.013206 freq pi(Q): 0.017035 freq pi(E): 0.032910 freq pi(G): 0.040615 freq pi(H): 0.017320 freq pi(I): 0.076552 freq pi(L): 0.121089 freq pi(K): 0.081894 freq pi(M): 0.018295 freq pi(F): 0.138937 freq pi(P): 0.021362 freq pi(S): 0.074952 freq pi(T): 0.046781 freq pi(W): 0.015991 freq pi(Y): 0.054417 freq pi(V): 0.056786 ML search took 1346.058929 secs or 0.373905 hours Combined Bootstrap and ML search took 1835.516372 secs or 0.509866 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.95perc_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.95perc_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.95perc_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.95perc_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.95perc_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.95perc_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.95perc_cov Overall execution time for full ML analysis: 1835.570727 secs or 0.509881 hours or 0.021245 days