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 6329 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 19.29% 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: 6329 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.99perc_cov.fa -n RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 1319.660430 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 70.966462 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.886476 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Time for BS model parameter optimization 192.998573 Bootstrap[0]: Time 219.914562 seconds, bootstrap likelihood -108635.652017, best rearrangement setting 13 Bootstrap[1]: Time 23.752443 seconds, bootstrap likelihood -109447.164928, best rearrangement setting 13 Bootstrap[2]: Time 23.851525 seconds, bootstrap likelihood -108721.981615, best rearrangement setting 12 Bootstrap[3]: Time 26.681348 seconds, bootstrap likelihood -108401.015112, best rearrangement setting 15 Bootstrap[4]: Time 25.234690 seconds, bootstrap likelihood -108434.425724, best rearrangement setting 10 Bootstrap[5]: Time 7.556016 seconds, bootstrap likelihood -108018.784237, best rearrangement setting 10 Bootstrap[6]: Time 24.269592 seconds, bootstrap likelihood -108510.422942, best rearrangement setting 6 Bootstrap[7]: Time 7.033664 seconds, bootstrap likelihood -107811.525928, best rearrangement setting 14 Bootstrap[8]: Time 24.510158 seconds, bootstrap likelihood -108630.602509, best rearrangement setting 5 Bootstrap[9]: Time 8.085418 seconds, bootstrap likelihood -109505.084272, best rearrangement setting 7 Bootstrap[10]: Time 23.333325 seconds, bootstrap likelihood -109306.538203, best rearrangement setting 7 Bootstrap[11]: Time 23.437210 seconds, bootstrap likelihood -107277.892067, best rearrangement setting 5 Bootstrap[12]: Time 25.876912 seconds, bootstrap likelihood -107759.672674, best rearrangement setting 8 Bootstrap[13]: Time 7.622746 seconds, bootstrap likelihood -108404.493621, best rearrangement setting 7 Bootstrap[14]: Time 24.885776 seconds, bootstrap likelihood -108151.779249, best rearrangement setting 12 Bootstrap[15]: Time 24.565825 seconds, bootstrap likelihood -107737.358521, best rearrangement setting 15 Bootstrap[16]: Time 7.413241 seconds, bootstrap likelihood -108440.099767, best rearrangement setting 12 Bootstrap[17]: Time 24.733652 seconds, bootstrap likelihood -108932.413061, best rearrangement setting 12 Bootstrap[18]: Time 21.666243 seconds, bootstrap likelihood -108413.317292, best rearrangement setting 5 Bootstrap[19]: Time 25.556415 seconds, bootstrap likelihood -107788.602684, best rearrangement setting 8 Bootstrap[20]: Time 23.076468 seconds, bootstrap likelihood -109787.305006, best rearrangement setting 10 Bootstrap[21]: Time 24.944656 seconds, bootstrap likelihood -108610.299468, best rearrangement setting 6 Bootstrap[22]: Time 23.475779 seconds, bootstrap likelihood -108560.676611, best rearrangement setting 5 Bootstrap[23]: Time 8.051731 seconds, bootstrap likelihood -108716.403770, best rearrangement setting 7 Bootstrap[24]: Time 7.824783 seconds, bootstrap likelihood -106829.739353, best rearrangement setting 8 Bootstrap[25]: Time 24.186375 seconds, bootstrap likelihood -109374.267977, best rearrangement setting 6 Bootstrap[26]: Time 24.681555 seconds, bootstrap likelihood -108712.115241, best rearrangement setting 12 Bootstrap[27]: Time 7.235627 seconds, bootstrap likelihood -107787.997408, best rearrangement setting 10 Bootstrap[28]: Time 7.744930 seconds, bootstrap likelihood -107722.888448, best rearrangement setting 11 Bootstrap[29]: Time 24.181840 seconds, bootstrap likelihood -109296.190633, best rearrangement setting 12 Bootstrap[30]: Time 26.096472 seconds, bootstrap likelihood -106990.268119, best rearrangement setting 15 Bootstrap[31]: Time 7.903709 seconds, bootstrap likelihood -108998.160431, best rearrangement setting 15 Bootstrap[32]: Time 23.835483 seconds, bootstrap likelihood -107663.423207, best rearrangement setting 6 Bootstrap[33]: Time 7.614458 seconds, bootstrap likelihood -107591.685507, best rearrangement setting 15 Bootstrap[34]: Time 23.571944 seconds, bootstrap likelihood -108572.200312, best rearrangement setting 11 Bootstrap[35]: Time 23.034134 seconds, bootstrap likelihood -108040.813877, best rearrangement setting 8 Bootstrap[36]: Time 24.602868 seconds, bootstrap likelihood -107351.607052, best rearrangement setting 9 Bootstrap[37]: Time 24.796866 seconds, bootstrap likelihood -107891.267522, best rearrangement setting 11 Bootstrap[38]: Time 7.919253 seconds, bootstrap likelihood -108054.477066, best rearrangement setting 8 Bootstrap[39]: Time 7.656165 seconds, bootstrap likelihood -108036.506172, best rearrangement setting 13 Bootstrap[40]: Time 23.706557 seconds, bootstrap likelihood -108714.699997, best rearrangement setting 13 Bootstrap[41]: Time 7.874392 seconds, bootstrap likelihood -107571.018842, best rearrangement setting 10 Bootstrap[42]: Time 20.487687 seconds, bootstrap likelihood -107853.281435, best rearrangement setting 5 Bootstrap[43]: Time 25.123752 seconds, bootstrap likelihood -108287.913687, best rearrangement setting 14 Bootstrap[44]: Time 24.008212 seconds, bootstrap likelihood -108050.057769, best rearrangement setting 10 Bootstrap[45]: Time 23.945209 seconds, bootstrap likelihood -108150.666940, best rearrangement setting 15 Bootstrap[46]: Time 24.707338 seconds, bootstrap likelihood -108447.285151, best rearrangement setting 14 Bootstrap[47]: Time 23.525682 seconds, bootstrap likelihood -108297.938291, best rearrangement setting 8 Bootstrap[48]: Time 24.581896 seconds, bootstrap likelihood -109999.143873, best rearrangement setting 6 Bootstrap[49]: Time 7.176529 seconds, bootstrap likelihood -108603.742239, best rearrangement setting 7 Bootstrap[50]: Time 23.183749 seconds, bootstrap likelihood -109650.740955, best rearrangement setting 7 Bootstrap[51]: Time 7.599823 seconds, bootstrap likelihood -108386.760958, best rearrangement setting 11 Bootstrap[52]: Time 22.736505 seconds, bootstrap likelihood -108917.845879, best rearrangement setting 12 Bootstrap[53]: Time 24.975281 seconds, bootstrap likelihood -108484.416356, best rearrangement setting 8 Bootstrap[54]: Time 7.146005 seconds, bootstrap likelihood -108352.762593, best rearrangement setting 9 Bootstrap[55]: Time 7.543548 seconds, bootstrap likelihood -108667.987496, best rearrangement setting 11 Bootstrap[56]: Time 20.716450 seconds, bootstrap likelihood -108330.905342, best rearrangement setting 5 Bootstrap[57]: Time 24.408539 seconds, bootstrap likelihood -109444.130002, best rearrangement setting 7 Bootstrap[58]: Time 22.800799 seconds, bootstrap likelihood -108570.980568, best rearrangement setting 10 Bootstrap[59]: Time 22.969627 seconds, bootstrap likelihood -108597.095554, best rearrangement setting 9 Bootstrap[60]: Time 7.769086 seconds, bootstrap likelihood -107303.144786, best rearrangement setting 7 Bootstrap[61]: Time 22.860301 seconds, bootstrap likelihood -108069.426267, best rearrangement setting 5 Bootstrap[62]: Time 7.493668 seconds, bootstrap likelihood -108876.736708, best rearrangement setting 11 Bootstrap[63]: Time 23.686237 seconds, bootstrap likelihood -108342.167172, best rearrangement setting 12 Bootstrap[64]: Time 24.915151 seconds, bootstrap likelihood -108054.938115, best rearrangement setting 7 Bootstrap[65]: Time 23.304396 seconds, bootstrap likelihood -106731.674393, best rearrangement setting 5 Bootstrap[66]: Time 7.156026 seconds, bootstrap likelihood -107058.529581, best rearrangement setting 5 Bootstrap[67]: Time 24.552551 seconds, bootstrap likelihood -107566.956048, best rearrangement setting 15 Bootstrap[68]: Time 8.027759 seconds, bootstrap likelihood -109400.992307, best rearrangement setting 11 Bootstrap[69]: Time 21.589106 seconds, bootstrap likelihood -107615.901486, best rearrangement setting 5 Bootstrap[70]: Time 25.515022 seconds, bootstrap likelihood -109792.477609, best rearrangement setting 8 Bootstrap[71]: Time 7.772116 seconds, bootstrap likelihood -108109.248936, best rearrangement setting 10 Bootstrap[72]: Time 23.018287 seconds, bootstrap likelihood -108046.109452, best rearrangement setting 11 Bootstrap[73]: Time 7.060903 seconds, bootstrap likelihood -108123.494476, best rearrangement setting 9 Bootstrap[74]: Time 22.598729 seconds, bootstrap likelihood -108854.472988, best rearrangement setting 5 Bootstrap[75]: Time 23.497911 seconds, bootstrap likelihood -108647.428282, best rearrangement setting 8 Bootstrap[76]: Time 25.667156 seconds, bootstrap likelihood -109042.549867, best rearrangement setting 9 Bootstrap[77]: Time 23.428285 seconds, bootstrap likelihood -108062.138071, best rearrangement setting 11 Bootstrap[78]: Time 24.268616 seconds, bootstrap likelihood -108418.154707, best rearrangement setting 15 Bootstrap[79]: Time 23.796058 seconds, bootstrap likelihood -108315.593390, best rearrangement setting 9 Bootstrap[80]: Time 7.877904 seconds, bootstrap likelihood -108698.895509, best rearrangement setting 15 Bootstrap[81]: Time 23.296702 seconds, bootstrap likelihood -108216.155356, best rearrangement setting 7 Bootstrap[82]: Time 23.046359 seconds, bootstrap likelihood -110520.322632, best rearrangement setting 6 Bootstrap[83]: Time 25.071110 seconds, bootstrap likelihood -107340.761849, best rearrangement setting 10 Bootstrap[84]: Time 22.974137 seconds, bootstrap likelihood -108391.804067, best rearrangement setting 11 Bootstrap[85]: Time 24.793506 seconds, bootstrap likelihood -108289.179020, best rearrangement setting 8 Bootstrap[86]: Time 23.880933 seconds, bootstrap likelihood -108620.966955, best rearrangement setting 7 Bootstrap[87]: Time 7.989642 seconds, bootstrap likelihood -107790.253254, best rearrangement setting 7 Bootstrap[88]: Time 23.430193 seconds, bootstrap likelihood -109287.156221, best rearrangement setting 12 Bootstrap[89]: Time 23.631709 seconds, bootstrap likelihood -109849.907368, best rearrangement setting 10 Bootstrap[90]: Time 8.335157 seconds, bootstrap likelihood -108374.652694, best rearrangement setting 8 Bootstrap[91]: Time 7.283297 seconds, bootstrap likelihood -107819.562638, best rearrangement setting 12 Bootstrap[92]: Time 7.813587 seconds, bootstrap likelihood -108286.475687, best rearrangement setting 13 Bootstrap[93]: Time 24.578682 seconds, bootstrap likelihood -107976.620193, best rearrangement setting 15 Bootstrap[94]: Time 22.827421 seconds, bootstrap likelihood -108611.554469, best rearrangement setting 5 Bootstrap[95]: Time 22.261613 seconds, bootstrap likelihood -108325.616799, best rearrangement setting 5 Bootstrap[96]: Time 7.843358 seconds, bootstrap likelihood -107475.847839, best rearrangement setting 13 Bootstrap[97]: Time 24.907346 seconds, bootstrap likelihood -107627.004800, best rearrangement setting 11 Bootstrap[98]: Time 23.146594 seconds, bootstrap likelihood -108294.258057, best rearrangement setting 6 Bootstrap[99]: Time 24.578534 seconds, bootstrap likelihood -109492.005642, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 2099.471264 seconds Average Time per Rapid Bootstrap 20.994713 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 1322.988306 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 71.328722 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.924057 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.504100 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.078113 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 1675.074990 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1324.200339 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 71.596369 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.003150 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.506526 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.077548 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -108447.461486 Slow ML Search 1 Likelihood: -108447.461486 Slow ML Search 2 Likelihood: -108447.461486 Slow ML Search 3 Likelihood: -108447.461486 Slow ML Search 4 Likelihood: -108447.461486 Slow ML Search 5 Likelihood: -108447.461486 Slow ML Search 6 Likelihood: -108447.461486 Slow ML Search 7 Likelihood: -108447.461486 Slow ML Search 8 Likelihood: -108447.461486 Slow ML Search 9 Likelihood: -108447.461486 Slow ML optimization finished Slow ML search Time: 1109.400175 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1324.568082 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 71.691567 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.013098 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.505593 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.077069 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov_Partition_No Name Provided Thorough ML search Time: 416.340119 seconds Final ML Optimization Likelihood: -108447.467386 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.665662 Tree-Length: 16.151320 rate A <-> R: 0.480462 rate A <-> N: 0.606575 rate A <-> D: 1.696780 rate A <-> C: 5.835515 rate A <-> Q: 0.219656 rate A <-> E: 2.502282 rate A <-> G: 6.616815 rate A <-> H: 0.000000 rate A <-> I: 2.118554 rate A <-> L: 1.627844 rate A <-> K: 0.081462 rate A <-> M: 1.879725 rate A <-> F: 1.067006 rate A <-> P: 4.430277 rate A <-> S: 23.455453 rate A <-> T: 14.775467 rate A <-> W: 0.000000 rate A <-> Y: 0.008801 rate A <-> V: 13.282307 rate R <-> N: 0.761492 rate R <-> D: 0.000000 rate R <-> C: 0.960368 rate R <-> Q: 5.384885 rate R <-> E: 0.684962 rate R <-> G: 0.990301 rate R <-> H: 3.900652 rate R <-> I: 0.181426 rate R <-> L: 0.393947 rate R <-> K: 21.432743 rate R <-> M: 1.280186 rate R <-> F: 0.107946 rate R <-> P: 0.276400 rate R <-> S: 1.088149 rate R <-> T: 0.546157 rate R <-> W: 1.028095 rate R <-> Y: 0.413680 rate R <-> V: 0.000000 rate N <-> D: 15.099003 rate N <-> C: 0.484331 rate N <-> Q: 7.418873 rate N <-> E: 3.151006 rate N <-> G: 2.697917 rate N <-> H: 9.415378 rate N <-> I: 2.089841 rate N <-> L: 0.971733 rate N <-> K: 8.452523 rate N <-> M: 0.772445 rate N <-> F: 0.470494 rate N <-> P: 0.000000 rate N <-> S: 16.061030 rate N <-> T: 8.440057 rate N <-> W: 0.140759 rate N <-> Y: 3.634361 rate N <-> V: 0.430383 rate D <-> C: 1.102094 rate D <-> Q: 0.000000 rate D <-> E: 30.229626 rate D <-> G: 1.708224 rate D <-> H: 2.244346 rate D <-> I: 0.231307 rate D <-> L: 0.111328 rate D <-> K: 1.064418 rate D <-> M: 0.000000 rate D <-> F: 0.000000 rate D <-> P: 0.546446 rate D <-> S: 3.173182 rate D <-> T: 1.172582 rate D <-> W: 0.333413 rate D <-> Y: 0.691352 rate D <-> V: 0.083547 rate C <-> Q: 0.366157 rate C <-> E: 0.211536 rate C <-> G: 2.030089 rate C <-> H: 2.821557 rate C <-> I: 0.730531 rate C <-> L: 0.983221 rate C <-> K: 0.000000 rate C <-> M: 2.557991 rate C <-> F: 1.820404 rate C <-> P: 0.000000 rate C <-> S: 10.911916 rate C <-> T: 4.358138 rate C <-> W: 1.213765 rate C <-> Y: 3.644497 rate C <-> V: 5.612659 rate Q <-> E: 8.668351 rate Q <-> G: 0.000000 rate Q <-> H: 20.432797 rate Q <-> I: 0.513267 rate Q <-> L: 2.023915 rate Q <-> K: 6.669540 rate Q <-> M: 0.981777 rate Q <-> F: 0.050255 rate Q <-> P: 3.325768 rate Q <-> S: 1.311496 rate Q <-> T: 3.620657 rate Q <-> W: 0.000000 rate Q <-> Y: 1.996372 rate Q <-> V: 0.000000 rate E <-> G: 2.015684 rate E <-> H: 0.349194 rate E <-> I: 0.351537 rate E <-> L: 0.384547 rate E <-> K: 3.701356 rate E <-> M: 0.309184 rate E <-> F: 0.223463 rate E <-> P: 0.237484 rate E <-> S: 2.329701 rate E <-> T: 2.165653 rate E <-> W: 0.208490 rate E <-> Y: 1.115392 rate E <-> V: 0.413226 rate G <-> H: 0.690139 rate G <-> I: 0.157217 rate G <-> L: 0.037212 rate G <-> K: 0.453973 rate G <-> M: 0.440823 rate G <-> F: 0.274392 rate G <-> P: 0.000000 rate G <-> S: 6.237653 rate G <-> T: 0.323647 rate G <-> W: 0.951244 rate G <-> Y: 0.000000 rate G <-> V: 0.568707 rate H <-> I: 0.042238 rate H <-> L: 0.859478 rate H <-> K: 0.223680 rate H <-> M: 0.000000 rate H <-> F: 0.555900 rate H <-> P: 0.679480 rate H <-> S: 1.842866 rate H <-> T: 0.889644 rate H <-> W: 0.067046 rate H <-> Y: 10.497401 rate H <-> V: 0.000000 rate I <-> L: 17.810052 rate I <-> K: 1.205479 rate I <-> M: 15.659291 rate I <-> F: 3.434725 rate I <-> P: 0.234034 rate I <-> S: 0.724691 rate I <-> T: 8.324969 rate I <-> W: 0.349721 rate I <-> Y: 1.397554 rate I <-> V: 50.538000 rate L <-> K: 0.602611 rate L <-> M: 14.142109 rate L <-> F: 6.347964 rate L <-> P: 0.696466 rate L <-> S: 1.728908 rate L <-> T: 1.678593 rate L <-> W: 1.373647 rate L <-> Y: 1.112007 rate L <-> V: 4.478800 rate K <-> M: 0.626827 rate K <-> F: 0.086602 rate K <-> P: 0.337482 rate K <-> S: 1.829523 rate K <-> T: 2.122743 rate K <-> W: 0.091877 rate K <-> Y: 0.654643 rate K <-> V: 0.302382 rate M <-> F: 1.703149 rate M <-> P: 0.400801 rate M <-> S: 0.819224 rate M <-> T: 5.471027 rate M <-> W: 0.000000 rate M <-> Y: 0.188274 rate M <-> V: 7.072717 rate F <-> P: 0.263032 rate F <-> S: 1.369082 rate F <-> T: 0.674248 rate F <-> W: 1.280113 rate F <-> Y: 11.512492 rate F <-> V: 1.324032 rate P <-> S: 5.746230 rate P <-> T: 1.986558 rate P <-> W: 0.000000 rate P <-> Y: 0.603086 rate P <-> V: 0.972421 rate S <-> T: 24.256301 rate S <-> W: 0.429436 rate S <-> Y: 1.631369 rate S <-> V: 1.234508 rate T <-> W: 0.123278 rate T <-> Y: 1.334051 rate T <-> V: 11.413700 rate W <-> Y: 2.343868 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.043449 freq pi(R): 0.041227 freq pi(N): 0.061654 freq pi(D): 0.027734 freq pi(C): 0.013765 freq pi(Q): 0.017171 freq pi(E): 0.033568 freq pi(G): 0.042152 freq pi(H): 0.018510 freq pi(I): 0.076523 freq pi(L): 0.120533 freq pi(K): 0.081282 freq pi(M): 0.018690 freq pi(F): 0.132862 freq pi(P): 0.022913 freq pi(S): 0.073372 freq pi(T): 0.046676 freq pi(W): 0.015991 freq pi(Y): 0.054569 freq pi(V): 0.057360 ML search took 3200.916404 secs or 0.889143 hours Combined Bootstrap and ML search took 5300.388550 secs or 1.472330 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-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bootstrap.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov Best-scoring ML tree written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov Best-scoring ML tree with support values written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitions.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.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-PROTGAMMAGTR-supermatrix.mito.full-assemblies.99perc_cov Overall execution time for full ML analysis: 5300.458558 secs or 1.472350 hours or 0.061348 days