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 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: 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-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 1352.958433 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 62.082685 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.929280 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.99perc_cov_Partition_No Name Provided Time for BS model parameter optimization 148.503127 Bootstrap[0]: Time 155.399012 seconds, bootstrap likelihood -97420.536901, best rearrangement setting 13 Bootstrap[1]: Time 12.692289 seconds, bootstrap likelihood -99063.619536, best rearrangement setting 13 Bootstrap[2]: Time 13.684588 seconds, bootstrap likelihood -98027.865128, best rearrangement setting 12 Bootstrap[3]: Time 13.731646 seconds, bootstrap likelihood -96595.119055, best rearrangement setting 15 Bootstrap[4]: Time 5.348738 seconds, bootstrap likelihood -96497.803599, best rearrangement setting 10 Bootstrap[5]: Time 5.383397 seconds, bootstrap likelihood -96473.925725, best rearrangement setting 10 Bootstrap[6]: Time 12.142880 seconds, bootstrap likelihood -97538.982170, best rearrangement setting 6 Bootstrap[7]: Time 13.267631 seconds, bootstrap likelihood -98300.809500, best rearrangement setting 14 Bootstrap[8]: Time 5.149017 seconds, bootstrap likelihood -97494.125105, best rearrangement setting 5 Bootstrap[9]: Time 11.591450 seconds, bootstrap likelihood -96530.681366, best rearrangement setting 7 Bootstrap[10]: Time 6.015395 seconds, bootstrap likelihood -97641.764395, best rearrangement setting 7 Bootstrap[11]: Time 5.446097 seconds, bootstrap likelihood -96342.316817, best rearrangement setting 5 Bootstrap[12]: Time 4.962767 seconds, bootstrap likelihood -97713.749250, best rearrangement setting 8 Bootstrap[13]: Time 5.672201 seconds, bootstrap likelihood -96278.733448, best rearrangement setting 7 Bootstrap[14]: Time 13.211401 seconds, bootstrap likelihood -97557.579006, best rearrangement setting 12 Bootstrap[15]: Time 13.560902 seconds, bootstrap likelihood -95721.656905, best rearrangement setting 15 Bootstrap[16]: Time 5.642491 seconds, bootstrap likelihood -97503.379311, best rearrangement setting 12 Bootstrap[17]: Time 14.224884 seconds, bootstrap likelihood -99229.483965, best rearrangement setting 12 Bootstrap[18]: Time 5.301595 seconds, bootstrap likelihood -96865.277521, best rearrangement setting 5 Bootstrap[19]: Time 5.205483 seconds, bootstrap likelihood -97562.620790, best rearrangement setting 8 Bootstrap[20]: Time 13.918862 seconds, bootstrap likelihood -98328.669234, best rearrangement setting 10 Bootstrap[21]: Time 5.766389 seconds, bootstrap likelihood -97000.967493, best rearrangement setting 6 Bootstrap[22]: Time 4.996255 seconds, bootstrap likelihood -97611.451962, best rearrangement setting 5 Bootstrap[23]: Time 12.465143 seconds, bootstrap likelihood -97677.343196, best rearrangement setting 7 Bootstrap[24]: Time 13.918718 seconds, bootstrap likelihood -96729.780636, best rearrangement setting 8 Bootstrap[25]: Time 12.275442 seconds, bootstrap likelihood -98365.691149, best rearrangement setting 6 Bootstrap[26]: Time 12.664127 seconds, bootstrap likelihood -97584.974717, best rearrangement setting 12 Bootstrap[27]: Time 12.999878 seconds, bootstrap likelihood -97041.957257, best rearrangement setting 10 Bootstrap[28]: Time 13.108909 seconds, bootstrap likelihood -96622.482269, best rearrangement setting 11 Bootstrap[29]: Time 12.751948 seconds, bootstrap likelihood -97599.652907, best rearrangement setting 12 Bootstrap[30]: Time 13.608832 seconds, bootstrap likelihood -97170.561750, best rearrangement setting 15 Bootstrap[31]: Time 13.336434 seconds, bootstrap likelihood -97649.443044, best rearrangement setting 15 Bootstrap[32]: Time 12.011021 seconds, bootstrap likelihood -96456.302805, best rearrangement setting 6 Bootstrap[33]: Time 13.184434 seconds, bootstrap likelihood -97796.305141, best rearrangement setting 15 Bootstrap[34]: Time 14.290115 seconds, bootstrap likelihood -97297.748272, best rearrangement setting 11 Bootstrap[35]: Time 12.935166 seconds, bootstrap likelihood -96714.447384, best rearrangement setting 8 Bootstrap[36]: Time 5.547944 seconds, bootstrap likelihood -97520.067495, best rearrangement setting 9 Bootstrap[37]: Time 5.308300 seconds, bootstrap likelihood -97599.180474, best rearrangement setting 11 Bootstrap[38]: Time 5.667371 seconds, bootstrap likelihood -97062.507575, best rearrangement setting 8 Bootstrap[39]: Time 5.070150 seconds, bootstrap likelihood -98425.203560, best rearrangement setting 13 Bootstrap[40]: Time 5.342355 seconds, bootstrap likelihood -96508.139997, best rearrangement setting 13 Bootstrap[41]: Time 12.444384 seconds, bootstrap likelihood -97255.678993, best rearrangement setting 10 Bootstrap[42]: Time 12.409676 seconds, bootstrap likelihood -98205.728318, best rearrangement setting 5 Bootstrap[43]: Time 5.282327 seconds, bootstrap likelihood -98830.430524, best rearrangement setting 14 Bootstrap[44]: Time 4.921024 seconds, bootstrap likelihood -98468.207537, best rearrangement setting 10 Bootstrap[45]: Time 5.311380 seconds, bootstrap likelihood -98009.946612, best rearrangement setting 15 Bootstrap[46]: Time 12.881312 seconds, bootstrap likelihood -97586.508540, best rearrangement setting 14 Bootstrap[47]: Time 12.709140 seconds, bootstrap likelihood -98490.241242, best rearrangement setting 8 Bootstrap[48]: Time 12.660189 seconds, bootstrap likelihood -96780.405788, best rearrangement setting 6 Bootstrap[49]: Time 5.637340 seconds, bootstrap likelihood -97323.563625, best rearrangement setting 7 Bootstrap[50]: Time 5.515057 seconds, bootstrap likelihood -97499.193522, best rearrangement setting 7 Bootstrap[51]: Time 13.631805 seconds, bootstrap likelihood -97612.214928, best rearrangement setting 11 Bootstrap[52]: Time 13.338816 seconds, bootstrap likelihood -97778.785052, best rearrangement setting 12 Bootstrap[53]: Time 13.237701 seconds, bootstrap likelihood -98381.234024, best rearrangement setting 8 Bootstrap[54]: Time 5.043027 seconds, bootstrap likelihood -97120.074366, best rearrangement setting 9 Bootstrap[55]: Time 12.108163 seconds, bootstrap likelihood -97577.653004, best rearrangement setting 11 Bootstrap[56]: Time 12.982218 seconds, bootstrap likelihood -98596.260417, best rearrangement setting 5 Bootstrap[57]: Time 13.177265 seconds, bootstrap likelihood -97117.543500, best rearrangement setting 7 Bootstrap[58]: Time 13.195936 seconds, bootstrap likelihood -96165.890756, best rearrangement setting 10 Bootstrap[59]: Time 4.920048 seconds, bootstrap likelihood -96297.076288, best rearrangement setting 9 Bootstrap[60]: Time 12.704472 seconds, bootstrap likelihood -96230.626498, best rearrangement setting 7 Bootstrap[61]: Time 12.658301 seconds, bootstrap likelihood -98045.618583, best rearrangement setting 5 Bootstrap[62]: Time 13.347060 seconds, bootstrap likelihood -97781.354013, best rearrangement setting 11 Bootstrap[63]: Time 13.055827 seconds, bootstrap likelihood -96753.849432, best rearrangement setting 12 Bootstrap[64]: Time 12.742753 seconds, bootstrap likelihood -97288.713447, best rearrangement setting 7 Bootstrap[65]: Time 5.368987 seconds, bootstrap likelihood -96484.723209, best rearrangement setting 5 Bootstrap[66]: Time 13.466991 seconds, bootstrap likelihood -98705.496197, best rearrangement setting 5 Bootstrap[67]: Time 12.640968 seconds, bootstrap likelihood -98739.161891, best rearrangement setting 15 Bootstrap[68]: Time 5.503887 seconds, bootstrap likelihood -98251.326340, best rearrangement setting 11 Bootstrap[69]: Time 13.085907 seconds, bootstrap likelihood -98574.245481, best rearrangement setting 5 Bootstrap[70]: Time 13.583379 seconds, bootstrap likelihood -97825.492150, best rearrangement setting 8 Bootstrap[71]: Time 12.600500 seconds, bootstrap likelihood -96713.085615, best rearrangement setting 10 Bootstrap[72]: Time 12.823624 seconds, bootstrap likelihood -97547.302682, best rearrangement setting 11 Bootstrap[73]: Time 5.538118 seconds, bootstrap likelihood -97676.611824, best rearrangement setting 9 Bootstrap[74]: Time 13.098959 seconds, bootstrap likelihood -98300.775926, best rearrangement setting 5 Bootstrap[75]: Time 13.482350 seconds, bootstrap likelihood -97596.569324, best rearrangement setting 8 Bootstrap[76]: Time 13.652547 seconds, bootstrap likelihood -96743.471925, best rearrangement setting 9 Bootstrap[77]: Time 5.780459 seconds, bootstrap likelihood -96522.865988, best rearrangement setting 11 Bootstrap[78]: Time 12.709260 seconds, bootstrap likelihood -97632.439055, best rearrangement setting 15 Bootstrap[79]: Time 5.589406 seconds, bootstrap likelihood -97621.992161, best rearrangement setting 9 Bootstrap[80]: Time 13.338572 seconds, bootstrap likelihood -98992.845327, best rearrangement setting 15 Bootstrap[81]: Time 5.468544 seconds, bootstrap likelihood -97831.296464, best rearrangement setting 7 Bootstrap[82]: Time 5.123865 seconds, bootstrap likelihood -97117.736150, best rearrangement setting 6 Bootstrap[83]: Time 12.611634 seconds, bootstrap likelihood -96679.920217, best rearrangement setting 10 Bootstrap[84]: Time 11.703689 seconds, bootstrap likelihood -97793.740040, best rearrangement setting 11 Bootstrap[85]: Time 13.403487 seconds, bootstrap likelihood -97820.669165, best rearrangement setting 8 Bootstrap[86]: Time 12.580550 seconds, bootstrap likelihood -96998.224261, best rearrangement setting 7 Bootstrap[87]: Time 5.246204 seconds, bootstrap likelihood -97701.610976, best rearrangement setting 7 Bootstrap[88]: Time 12.279917 seconds, bootstrap likelihood -96599.860537, best rearrangement setting 12 Bootstrap[89]: Time 12.818036 seconds, bootstrap likelihood -96689.894100, best rearrangement setting 10 Bootstrap[90]: Time 13.569169 seconds, bootstrap likelihood -97379.085148, best rearrangement setting 8 Bootstrap[91]: Time 13.262876 seconds, bootstrap likelihood -97986.692965, best rearrangement setting 12 Bootstrap[92]: Time 12.613732 seconds, bootstrap likelihood -97424.487484, best rearrangement setting 13 Bootstrap[93]: Time 11.716382 seconds, bootstrap likelihood -97542.216405, best rearrangement setting 15 Bootstrap[94]: Time 13.020455 seconds, bootstrap likelihood -98121.587868, best rearrangement setting 5 Bootstrap[95]: Time 13.216144 seconds, bootstrap likelihood -98351.439301, best rearrangement setting 5 Bootstrap[96]: Time 13.369824 seconds, bootstrap likelihood -96876.890344, best rearrangement setting 13 Bootstrap[97]: Time 13.362883 seconds, bootstrap likelihood -97570.747907, best rearrangement setting 11 Bootstrap[98]: Time 12.384361 seconds, bootstrap likelihood -98172.261931, best rearrangement setting 6 Bootstrap[99]: Time 13.445431 seconds, bootstrap likelihood -96594.879973, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 1198.571796 seconds Average Time per Rapid Bootstrap 11.985718 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 1353.131097 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 62.131143 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.932725 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.143345 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.015613 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.99perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 1187.079881 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1361.136031 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 62.462766 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.008598 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.148898 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.016214 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.99perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -97639.276522 Slow ML Search 1 Likelihood: -97639.276522 Slow ML Search 2 Likelihood: -97639.276522 Slow ML Search 3 Likelihood: -97639.276520 Slow ML Search 4 Likelihood: -97639.276521 Slow ML Search 5 Likelihood: -97639.276520 Slow ML Search 6 Likelihood: -97639.276522 Slow ML Search 7 Likelihood: -97639.276522 Slow ML Search 8 Likelihood: -97639.276521 Slow ML Search 9 Likelihood: -97639.276521 Slow ML optimization finished Slow ML search Time: 776.621513 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1361.204144 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 62.722186 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.020320 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.149121 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.016203 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.99perc_cov_Partition_No Name Provided Thorough ML search Time: 307.580937 seconds Final ML Optimization Likelihood: -97639.271164 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.589978 Tree-Length: 5.470553 rate A <-> R: 0.465014 rate A <-> N: 0.697276 rate A <-> D: 1.900149 rate A <-> C: 3.548924 rate A <-> Q: 0.143941 rate A <-> E: 3.028508 rate A <-> G: 5.213262 rate A <-> H: 0.000000 rate A <-> I: 2.101059 rate A <-> L: 1.182303 rate A <-> K: 0.092224 rate A <-> M: 1.244316 rate A <-> F: 1.173316 rate A <-> P: 4.458533 rate A <-> S: 23.120649 rate A <-> T: 14.661636 rate A <-> W: 0.000000 rate A <-> Y: 0.000000 rate A <-> V: 13.483511 rate R <-> N: 0.266713 rate R <-> D: 0.000000 rate R <-> C: 0.497265 rate R <-> Q: 5.464461 rate R <-> E: 0.721387 rate R <-> G: 1.056179 rate R <-> H: 3.024789 rate R <-> I: 0.085236 rate R <-> L: 0.448840 rate R <-> K: 22.688890 rate R <-> M: 0.992288 rate R <-> F: 0.136557 rate R <-> P: 0.162418 rate R <-> S: 1.131481 rate R <-> T: 0.594990 rate R <-> W: 0.491898 rate R <-> Y: 0.220012 rate R <-> V: 0.000000 rate N <-> D: 15.105251 rate N <-> C: 0.967111 rate N <-> Q: 7.463719 rate N <-> E: 2.964109 rate N <-> G: 2.568624 rate N <-> H: 9.892690 rate N <-> I: 2.195640 rate N <-> L: 0.948987 rate N <-> K: 8.610709 rate N <-> M: 0.863674 rate N <-> F: 0.505701 rate N <-> P: 0.000000 rate N <-> S: 16.384543 rate N <-> T: 8.273200 rate N <-> W: 0.169085 rate N <-> Y: 3.754632 rate N <-> V: 0.471320 rate D <-> C: 0.971416 rate D <-> Q: 0.000000 rate D <-> E: 32.252382 rate D <-> G: 2.038284 rate D <-> H: 1.901601 rate D <-> I: 0.168351 rate D <-> L: 0.140994 rate D <-> K: 1.017670 rate D <-> M: 0.356693 rate D <-> F: 0.000000 rate D <-> P: 0.516651 rate D <-> S: 3.064261 rate D <-> T: 1.023907 rate D <-> W: 0.288555 rate D <-> Y: 0.845546 rate D <-> V: 0.138436 rate C <-> Q: 0.000000 rate C <-> E: 0.413610 rate C <-> G: 2.404297 rate C <-> H: 2.850816 rate C <-> I: 0.600578 rate C <-> L: 0.847455 rate C <-> K: 0.000000 rate C <-> M: 2.823888 rate C <-> F: 1.855366 rate C <-> P: 0.000000 rate C <-> S: 11.904470 rate C <-> T: 3.235037 rate C <-> W: 0.572877 rate C <-> Y: 4.114149 rate C <-> V: 4.936806 rate Q <-> E: 8.538993 rate Q <-> G: 0.000000 rate Q <-> H: 19.200298 rate Q <-> I: 0.512201 rate Q <-> L: 2.235529 rate Q <-> K: 6.465791 rate Q <-> M: 0.774873 rate Q <-> F: 0.000000 rate Q <-> P: 3.132941 rate Q <-> S: 1.344502 rate Q <-> T: 1.629664 rate Q <-> W: 0.033371 rate Q <-> Y: 2.137164 rate Q <-> V: 0.000000 rate E <-> G: 2.207227 rate E <-> H: 0.216718 rate E <-> I: 0.176406 rate E <-> L: 0.463218 rate E <-> K: 3.962320 rate E <-> M: 0.000000 rate E <-> F: 0.187021 rate E <-> P: 0.238579 rate E <-> S: 2.247783 rate E <-> T: 2.048383 rate E <-> W: 0.197826 rate E <-> Y: 0.960248 rate E <-> V: 0.433013 rate G <-> H: 0.731962 rate G <-> I: 0.151131 rate G <-> L: 0.032832 rate G <-> K: 0.357940 rate G <-> M: 0.134448 rate G <-> F: 0.299459 rate G <-> P: 0.000000 rate G <-> S: 6.155424 rate G <-> T: 0.273721 rate G <-> W: 0.579920 rate G <-> Y: 0.000000 rate G <-> V: 0.505473 rate H <-> I: 0.069977 rate H <-> L: 0.693951 rate H <-> K: 0.225132 rate H <-> M: 0.000000 rate H <-> F: 0.622710 rate H <-> P: 0.500849 rate H <-> S: 1.555806 rate H <-> T: 0.805029 rate H <-> W: 0.000000 rate H <-> Y: 11.909981 rate H <-> V: 0.000000 rate I <-> L: 17.576354 rate I <-> K: 1.204682 rate I <-> M: 16.180141 rate I <-> F: 3.404035 rate I <-> P: 0.195038 rate I <-> S: 0.897866 rate I <-> T: 8.862690 rate I <-> W: 0.358094 rate I <-> Y: 1.474185 rate I <-> V: 51.566488 rate L <-> K: 0.614003 rate L <-> M: 13.574267 rate L <-> F: 6.248876 rate L <-> P: 0.738730 rate L <-> S: 1.728316 rate L <-> T: 1.601300 rate L <-> W: 1.160427 rate L <-> Y: 1.105656 rate L <-> V: 4.209574 rate K <-> M: 0.746858 rate K <-> F: 0.078582 rate K <-> P: 0.369765 rate K <-> S: 1.831363 rate K <-> T: 2.077236 rate K <-> W: 0.147963 rate K <-> Y: 0.614694 rate K <-> V: 0.323670 rate M <-> F: 1.356901 rate M <-> P: 0.200525 rate M <-> S: 0.880337 rate M <-> T: 6.013046 rate M <-> W: 0.407764 rate M <-> Y: 0.398775 rate M <-> V: 7.545406 rate F <-> P: 0.209591 rate F <-> S: 1.378976 rate F <-> T: 0.635370 rate F <-> W: 0.848078 rate F <-> Y: 11.424747 rate F <-> V: 1.284087 rate P <-> S: 5.797393 rate P <-> T: 1.896723 rate P <-> W: 0.355780 rate P <-> Y: 0.720531 rate P <-> V: 0.695151 rate S <-> T: 23.655987 rate S <-> W: 0.349829 rate S <-> Y: 1.615723 rate S <-> V: 1.067415 rate T <-> W: 0.000000 rate T <-> Y: 1.497469 rate T <-> V: 11.700470 rate W <-> Y: 1.093826 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 2271.382701 secs or 0.630940 hours Combined Bootstrap and ML search took 3469.958716 secs or 0.963877 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.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.Oligohymenophorea.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.Oligohymenophorea.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.Oligohymenophorea.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.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-PROTGAMMAGTR-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-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.99perc_cov Overall execution time for full ML analysis: 3470.044780 secs or 0.963901 hours or 0.040163 days