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 8557 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 15.02% 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: 8557 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.50perc_cov.fa -n RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 2148.460707 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 113.272147 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 6.177096 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.379549 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Time for BS model parameter optimization 307.119148 Bootstrap[0]: Time 329.613180 seconds, bootstrap likelihood -161040.680949, best rearrangement setting 13 Bootstrap[1]: Time 9.226359 seconds, bootstrap likelihood -159571.891415, best rearrangement setting 13 Bootstrap[2]: Time 20.700227 seconds, bootstrap likelihood -161452.808268, best rearrangement setting 12 Bootstrap[3]: Time 21.221345 seconds, bootstrap likelihood -163704.427733, best rearrangement setting 15 Bootstrap[4]: Time 21.236051 seconds, bootstrap likelihood -161663.843974, best rearrangement setting 10 Bootstrap[5]: Time 21.634352 seconds, bootstrap likelihood -161675.468746, best rearrangement setting 10 Bootstrap[6]: Time 21.145137 seconds, bootstrap likelihood -162869.420226, best rearrangement setting 6 Bootstrap[7]: Time 21.674839 seconds, bootstrap likelihood -161416.972329, best rearrangement setting 14 Bootstrap[8]: Time 20.115957 seconds, bootstrap likelihood -161383.764497, best rearrangement setting 5 Bootstrap[9]: Time 9.476754 seconds, bootstrap likelihood -163240.184868, best rearrangement setting 7 Bootstrap[10]: Time 21.818673 seconds, bootstrap likelihood -162463.816439, best rearrangement setting 7 Bootstrap[11]: Time 22.289256 seconds, bootstrap likelihood -163581.472959, best rearrangement setting 5 Bootstrap[12]: Time 21.562330 seconds, bootstrap likelihood -162468.662373, best rearrangement setting 8 Bootstrap[13]: Time 20.915235 seconds, bootstrap likelihood -163663.777964, best rearrangement setting 7 Bootstrap[14]: Time 21.162027 seconds, bootstrap likelihood -163214.467516, best rearrangement setting 12 Bootstrap[15]: Time 21.993345 seconds, bootstrap likelihood -163462.424266, best rearrangement setting 15 Bootstrap[16]: Time 21.884457 seconds, bootstrap likelihood -161812.437613, best rearrangement setting 12 Bootstrap[17]: Time 22.866837 seconds, bootstrap likelihood -163348.001522, best rearrangement setting 12 Bootstrap[18]: Time 21.642105 seconds, bootstrap likelihood -161242.025261, best rearrangement setting 5 Bootstrap[19]: Time 21.707474 seconds, bootstrap likelihood -162219.060692, best rearrangement setting 8 Bootstrap[20]: Time 23.171701 seconds, bootstrap likelihood -161047.136905, best rearrangement setting 10 Bootstrap[21]: Time 21.680346 seconds, bootstrap likelihood -162375.128215, best rearrangement setting 6 Bootstrap[22]: Time 20.223532 seconds, bootstrap likelihood -162638.633973, best rearrangement setting 5 Bootstrap[23]: Time 8.902293 seconds, bootstrap likelihood -161878.140859, best rearrangement setting 7 Bootstrap[24]: Time 24.091735 seconds, bootstrap likelihood -162869.287066, best rearrangement setting 8 Bootstrap[25]: Time 22.165372 seconds, bootstrap likelihood -161707.717687, best rearrangement setting 6 Bootstrap[26]: Time 9.991077 seconds, bootstrap likelihood -163103.847751, best rearrangement setting 12 Bootstrap[27]: Time 23.327817 seconds, bootstrap likelihood -162034.265189, best rearrangement setting 10 Bootstrap[28]: Time 21.889895 seconds, bootstrap likelihood -162022.639070, best rearrangement setting 11 Bootstrap[29]: Time 21.916111 seconds, bootstrap likelihood -162708.304917, best rearrangement setting 12 Bootstrap[30]: Time 23.239155 seconds, bootstrap likelihood -163390.631173, best rearrangement setting 15 Bootstrap[31]: Time 22.726908 seconds, bootstrap likelihood -162074.647341, best rearrangement setting 15 Bootstrap[32]: Time 9.183998 seconds, bootstrap likelihood -163202.538007, best rearrangement setting 6 Bootstrap[33]: Time 23.225977 seconds, bootstrap likelihood -162145.227592, best rearrangement setting 15 Bootstrap[34]: Time 22.968178 seconds, bootstrap likelihood -161975.103740, best rearrangement setting 11 Bootstrap[35]: Time 21.567840 seconds, bootstrap likelihood -160874.807505, best rearrangement setting 8 Bootstrap[36]: Time 22.358946 seconds, bootstrap likelihood -160626.243674, best rearrangement setting 9 Bootstrap[37]: Time 21.641559 seconds, bootstrap likelihood -162821.895752, best rearrangement setting 11 Bootstrap[38]: Time 22.351285 seconds, bootstrap likelihood -163370.020652, best rearrangement setting 8 Bootstrap[39]: Time 22.279467 seconds, bootstrap likelihood -163573.807304, best rearrangement setting 13 Bootstrap[40]: Time 9.607883 seconds, bootstrap likelihood -161546.119695, best rearrangement setting 13 Bootstrap[41]: Time 22.085223 seconds, bootstrap likelihood -161812.520340, best rearrangement setting 10 Bootstrap[42]: Time 21.140461 seconds, bootstrap likelihood -164102.295535, best rearrangement setting 5 Bootstrap[43]: Time 21.014341 seconds, bootstrap likelihood -163518.345992, best rearrangement setting 14 Bootstrap[44]: Time 22.342212 seconds, bootstrap likelihood -160327.594272, best rearrangement setting 10 Bootstrap[45]: Time 8.949860 seconds, bootstrap likelihood -162789.688717, best rearrangement setting 15 Bootstrap[46]: Time 21.864948 seconds, bootstrap likelihood -160901.012677, best rearrangement setting 14 Bootstrap[47]: Time 20.629964 seconds, bootstrap likelihood -162947.518904, best rearrangement setting 8 Bootstrap[48]: Time 22.182453 seconds, bootstrap likelihood -162519.371435, best rearrangement setting 6 Bootstrap[49]: Time 20.544451 seconds, bootstrap likelihood -162020.319490, best rearrangement setting 7 Bootstrap[50]: Time 22.809402 seconds, bootstrap likelihood -163801.193959, best rearrangement setting 7 Bootstrap[51]: Time 22.028660 seconds, bootstrap likelihood -163147.264849, best rearrangement setting 11 Bootstrap[52]: Time 21.918372 seconds, bootstrap likelihood -164423.061666, best rearrangement setting 12 Bootstrap[53]: Time 22.293919 seconds, bootstrap likelihood -161522.492866, best rearrangement setting 8 Bootstrap[54]: Time 22.016535 seconds, bootstrap likelihood -161365.204815, best rearrangement setting 9 Bootstrap[55]: Time 21.966510 seconds, bootstrap likelihood -162718.894499, best rearrangement setting 11 Bootstrap[56]: Time 21.233929 seconds, bootstrap likelihood -164833.205832, best rearrangement setting 5 Bootstrap[57]: Time 22.798723 seconds, bootstrap likelihood -162090.984577, best rearrangement setting 7 Bootstrap[58]: Time 20.437339 seconds, bootstrap likelihood -162550.896768, best rearrangement setting 10 Bootstrap[59]: Time 21.274825 seconds, bootstrap likelihood -163964.059776, best rearrangement setting 9 Bootstrap[60]: Time 23.413460 seconds, bootstrap likelihood -161228.619674, best rearrangement setting 7 Bootstrap[61]: Time 21.947514 seconds, bootstrap likelihood -160961.363862, best rearrangement setting 5 Bootstrap[62]: Time 22.758386 seconds, bootstrap likelihood -160700.249697, best rearrangement setting 11 Bootstrap[63]: Time 21.288199 seconds, bootstrap likelihood -163106.071393, best rearrangement setting 12 Bootstrap[64]: Time 24.437896 seconds, bootstrap likelihood -161239.840876, best rearrangement setting 7 Bootstrap[65]: Time 21.554935 seconds, bootstrap likelihood -161942.454600, best rearrangement setting 5 Bootstrap[66]: Time 21.131216 seconds, bootstrap likelihood -161210.285642, best rearrangement setting 5 Bootstrap[67]: Time 21.703047 seconds, bootstrap likelihood -161747.733541, best rearrangement setting 15 Bootstrap[68]: Time 22.380440 seconds, bootstrap likelihood -163425.450799, best rearrangement setting 11 Bootstrap[69]: Time 9.951305 seconds, bootstrap likelihood -162338.810326, best rearrangement setting 5 Bootstrap[70]: Time 22.385605 seconds, bootstrap likelihood -163823.449351, best rearrangement setting 8 Bootstrap[71]: Time 23.394981 seconds, bootstrap likelihood -161835.479932, best rearrangement setting 10 Bootstrap[72]: Time 23.007876 seconds, bootstrap likelihood -163580.094959, best rearrangement setting 11 Bootstrap[73]: Time 22.812794 seconds, bootstrap likelihood -161639.117487, best rearrangement setting 9 Bootstrap[74]: Time 21.905053 seconds, bootstrap likelihood -163228.241481, best rearrangement setting 5 Bootstrap[75]: Time 21.916964 seconds, bootstrap likelihood -161325.803514, best rearrangement setting 8 Bootstrap[76]: Time 22.136115 seconds, bootstrap likelihood -162296.539625, best rearrangement setting 9 Bootstrap[77]: Time 21.458492 seconds, bootstrap likelihood -162334.619390, best rearrangement setting 11 Bootstrap[78]: Time 22.526530 seconds, bootstrap likelihood -162383.366032, best rearrangement setting 15 Bootstrap[79]: Time 20.413532 seconds, bootstrap likelihood -162407.436866, best rearrangement setting 9 Bootstrap[80]: Time 20.546385 seconds, bootstrap likelihood -162940.236879, best rearrangement setting 15 Bootstrap[81]: Time 22.373153 seconds, bootstrap likelihood -163453.416205, best rearrangement setting 7 Bootstrap[82]: Time 21.954769 seconds, bootstrap likelihood -162187.151313, best rearrangement setting 6 Bootstrap[83]: Time 22.301745 seconds, bootstrap likelihood -161619.715698, best rearrangement setting 10 Bootstrap[84]: Time 22.207548 seconds, bootstrap likelihood -162042.253123, best rearrangement setting 11 Bootstrap[85]: Time 22.035414 seconds, bootstrap likelihood -162054.000042, best rearrangement setting 8 Bootstrap[86]: Time 21.425234 seconds, bootstrap likelihood -163323.707596, best rearrangement setting 7 Bootstrap[87]: Time 21.013476 seconds, bootstrap likelihood -161973.787975, best rearrangement setting 7 Bootstrap[88]: Time 20.630131 seconds, bootstrap likelihood -162286.007003, best rearrangement setting 12 Bootstrap[89]: Time 20.364604 seconds, bootstrap likelihood -163104.436111, best rearrangement setting 10 Bootstrap[90]: Time 23.238808 seconds, bootstrap likelihood -163200.298786, best rearrangement setting 8 Bootstrap[91]: Time 22.552140 seconds, bootstrap likelihood -161097.444281, best rearrangement setting 12 Bootstrap[92]: Time 21.699205 seconds, bootstrap likelihood -162562.017654, best rearrangement setting 13 Bootstrap[93]: Time 23.088886 seconds, bootstrap likelihood -162859.786757, best rearrangement setting 15 Bootstrap[94]: Time 21.866972 seconds, bootstrap likelihood -162114.773363, best rearrangement setting 5 Bootstrap[95]: Time 20.547377 seconds, bootstrap likelihood -162831.364915, best rearrangement setting 5 Bootstrap[96]: Time 23.891502 seconds, bootstrap likelihood -163617.371929, best rearrangement setting 13 Bootstrap[97]: Time 24.699303 seconds, bootstrap likelihood -162133.083192, best rearrangement setting 11 Bootstrap[98]: Time 23.018774 seconds, bootstrap likelihood -163512.404591, best rearrangement setting 6 Bootstrap[99]: Time 20.653636 seconds, bootstrap likelihood -162312.974481, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 2405.032448 seconds Average Time per Rapid Bootstrap 24.050324 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 2149.936392 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 113.494822 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 6.196247 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.381518 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.039948 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 2256.341222 seconds Printed linked AA GTR matrix that achieved an overall improvement of 2148.736337 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 113.370051 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 6.186504 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.380562 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.039857 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -162454.716451 Slow ML Search 1 Likelihood: -162454.716451 Slow ML Search 2 Likelihood: -162454.716451 Slow ML Search 3 Likelihood: -162454.716451 Slow ML Search 4 Likelihood: -162454.716451 Slow ML Search 5 Likelihood: -162454.716451 Slow ML Search 6 Likelihood: -162454.716451 Slow ML Search 7 Likelihood: -162454.716452 Slow ML Search 8 Likelihood: -162454.716451 Slow ML Search 9 Likelihood: -162454.716450 Slow ML optimization finished Slow ML search Time: 1194.544514 seconds Printed linked AA GTR matrix that achieved an overall improvement of 2148.984890 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 113.324681 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 6.185726 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.379745 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.039694 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.Oligohymenophorea.50perc_cov_Partition_No Name Provided Thorough ML search Time: 496.284133 seconds Final ML Optimization Likelihood: -162454.728403 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.567186 Tree-Length: 7.822820 rate A <-> R: 0.414534 rate A <-> N: 0.524604 rate A <-> D: 3.047120 rate A <-> C: 4.571977 rate A <-> Q: 0.465376 rate A <-> E: 3.807116 rate A <-> G: 7.274413 rate A <-> H: 0.153365 rate A <-> I: 1.938988 rate A <-> L: 1.340264 rate A <-> K: 0.254683 rate A <-> M: 1.100362 rate A <-> F: 0.952404 rate A <-> P: 5.334699 rate A <-> S: 21.944514 rate A <-> T: 16.131666 rate A <-> W: 0.136674 rate A <-> Y: 0.022952 rate A <-> V: 14.840150 rate R <-> N: 0.148252 rate R <-> D: 0.087990 rate R <-> C: 1.215257 rate R <-> Q: 6.596712 rate R <-> E: 0.984740 rate R <-> G: 2.053727 rate R <-> H: 4.323643 rate R <-> I: 0.293094 rate R <-> L: 0.510934 rate R <-> K: 22.658153 rate R <-> M: 1.106802 rate R <-> F: 0.132417 rate R <-> P: 0.927073 rate R <-> S: 1.402190 rate R <-> T: 0.687298 rate R <-> W: 0.905536 rate R <-> Y: 0.281001 rate R <-> V: 0.000000 rate N <-> D: 14.595307 rate N <-> C: 1.102230 rate N <-> Q: 6.674032 rate N <-> E: 2.756214 rate N <-> G: 2.315801 rate N <-> H: 8.518863 rate N <-> I: 2.830326 rate N <-> L: 0.833217 rate N <-> K: 8.549114 rate N <-> M: 0.620045 rate N <-> F: 0.609597 rate N <-> P: 0.291278 rate N <-> S: 15.219683 rate N <-> T: 8.579235 rate N <-> W: 0.195501 rate N <-> Y: 3.577018 rate N <-> V: 0.357549 rate D <-> C: 0.704208 rate D <-> Q: 0.038944 rate D <-> E: 34.256448 rate D <-> G: 3.938850 rate D <-> H: 1.440469 rate D <-> I: 0.218046 rate D <-> L: 0.207802 rate D <-> K: 1.079614 rate D <-> M: 0.249966 rate D <-> F: 0.127530 rate D <-> P: 1.506036 rate D <-> S: 3.474360 rate D <-> T: 1.790908 rate D <-> W: 0.164754 rate D <-> Y: 0.719988 rate D <-> V: 0.447197 rate C <-> Q: 0.000000 rate C <-> E: 0.000000 rate C <-> G: 3.315505 rate C <-> H: 3.385828 rate C <-> I: 1.035036 rate C <-> L: 1.177569 rate C <-> K: 0.000000 rate C <-> M: 2.325921 rate C <-> F: 1.801107 rate C <-> P: 0.051346 rate C <-> S: 9.688446 rate C <-> T: 2.768102 rate C <-> W: 0.780576 rate C <-> Y: 5.304682 rate C <-> V: 4.110344 rate Q <-> E: 8.987181 rate Q <-> G: 0.000000 rate Q <-> H: 24.759792 rate Q <-> I: 0.586984 rate Q <-> L: 1.833939 rate Q <-> K: 7.372213 rate Q <-> M: 1.822327 rate Q <-> F: 0.347363 rate Q <-> P: 3.982859 rate Q <-> S: 2.463670 rate Q <-> T: 1.424031 rate Q <-> W: 0.000000 rate Q <-> Y: 1.947758 rate Q <-> V: 0.198700 rate E <-> G: 4.045870 rate E <-> H: 1.137964 rate E <-> I: 0.145500 rate E <-> L: 0.378716 rate E <-> K: 4.253361 rate E <-> M: 0.000000 rate E <-> F: 0.077012 rate E <-> P: 1.246011 rate E <-> S: 2.266597 rate E <-> T: 1.676983 rate E <-> W: 0.141939 rate E <-> Y: 0.622009 rate E <-> V: 1.220369 rate G <-> H: 0.681248 rate G <-> I: 0.132675 rate G <-> L: 0.055760 rate G <-> K: 0.327714 rate G <-> M: 0.089158 rate G <-> F: 0.273370 rate G <-> P: 0.133222 rate G <-> S: 6.752590 rate G <-> T: 0.526578 rate G <-> W: 0.936240 rate G <-> Y: 0.000000 rate G <-> V: 0.913256 rate H <-> I: 0.164902 rate H <-> L: 1.043732 rate H <-> K: 0.462380 rate H <-> M: 0.000000 rate H <-> F: 0.564026 rate H <-> P: 1.357962 rate H <-> S: 1.800186 rate H <-> T: 1.766040 rate H <-> W: 0.470296 rate H <-> Y: 14.474708 rate H <-> V: 0.000000 rate I <-> L: 16.721656 rate I <-> K: 1.539484 rate I <-> M: 16.748620 rate I <-> F: 3.301380 rate I <-> P: 0.013876 rate I <-> S: 1.128234 rate I <-> T: 9.062078 rate I <-> W: 0.385460 rate I <-> Y: 2.371940 rate I <-> V: 48.920222 rate L <-> K: 0.613087 rate L <-> M: 13.216265 rate L <-> F: 5.869383 rate L <-> P: 1.530121 rate L <-> S: 1.795993 rate L <-> T: 1.776784 rate L <-> W: 1.318589 rate L <-> Y: 1.274259 rate L <-> V: 4.504379 rate K <-> M: 0.619270 rate K <-> F: 0.132959 rate K <-> P: 0.573843 rate K <-> S: 1.951954 rate K <-> T: 1.815593 rate K <-> W: 0.182665 rate K <-> Y: 0.768641 rate K <-> V: 0.335329 rate M <-> F: 1.154659 rate M <-> P: 0.000000 rate M <-> S: 0.716047 rate M <-> T: 5.875267 rate M <-> W: 0.378590 rate M <-> Y: 1.006857 rate M <-> V: 8.076458 rate F <-> P: 0.240543 rate F <-> S: 1.335590 rate F <-> T: 0.654305 rate F <-> W: 0.986981 rate F <-> Y: 9.842278 rate F <-> V: 1.331621 rate P <-> S: 6.894825 rate P <-> T: 3.657189 rate P <-> W: 0.379624 rate P <-> Y: 1.013574 rate P <-> V: 1.481982 rate S <-> T: 21.368406 rate S <-> W: 0.368407 rate S <-> Y: 1.570043 rate S <-> V: 1.410219 rate T <-> W: 0.000000 rate T <-> Y: 0.862439 rate T <-> V: 11.961948 rate W <-> Y: 1.634392 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.042956 freq pi(R): 0.037171 freq pi(N): 0.064863 freq pi(D): 0.029496 freq pi(C): 0.012366 freq pi(Q): 0.017418 freq pi(E): 0.036624 freq pi(G): 0.039462 freq pi(H): 0.016618 freq pi(I): 0.074237 freq pi(L): 0.123781 freq pi(K): 0.081814 freq pi(M): 0.016969 freq pi(F): 0.142345 freq pi(P): 0.021619 freq pi(S): 0.074493 freq pi(T): 0.044572 freq pi(W): 0.015216 freq pi(Y): 0.053513 freq pi(V): 0.054467 ML search took 3947.257476 secs or 1.096460 hours Combined Bootstrap and ML search took 6352.290710 secs or 1.764525 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.Oligohymenophorea.50perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_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.Oligohymenophorea.50perc_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.Oligohymenophorea.50perc_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.Oligohymenophorea.50perc_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.Oligohymenophorea.50perc_cov Overall execution time for full ML analysis: 6352.388359 secs or 1.764552 hours or 0.073523 days