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 7263 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 13.06% 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: 7263 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.90perc_cov.fa -n RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.90perc_cov -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 1823.875396 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 79.207554 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.332691 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.90perc_cov_Partition_No Name Provided Time for BS model parameter optimization 200.263614 Bootstrap[0]: Time 218.762749 seconds, bootstrap likelihood -136504.557972, best rearrangement setting 13 Bootstrap[1]: Time 16.951523 seconds, bootstrap likelihood -136266.654679, best rearrangement setting 13 Bootstrap[2]: Time 16.269604 seconds, bootstrap likelihood -137825.431628, best rearrangement setting 12 Bootstrap[3]: Time 6.802602 seconds, bootstrap likelihood -136796.292704, best rearrangement setting 15 Bootstrap[4]: Time 7.110311 seconds, bootstrap likelihood -138646.120338, best rearrangement setting 10 Bootstrap[5]: Time 16.928370 seconds, bootstrap likelihood -138262.530943, best rearrangement setting 10 Bootstrap[6]: Time 6.942440 seconds, bootstrap likelihood -137653.501446, best rearrangement setting 6 Bootstrap[7]: Time 16.586353 seconds, bootstrap likelihood -137890.441018, best rearrangement setting 14 Bootstrap[8]: Time 16.155834 seconds, bootstrap likelihood -137843.806669, best rearrangement setting 5 Bootstrap[9]: Time 17.907831 seconds, bootstrap likelihood -137565.546125, best rearrangement setting 7 Bootstrap[10]: Time 17.978303 seconds, bootstrap likelihood -137738.455905, best rearrangement setting 7 Bootstrap[11]: Time 17.806225 seconds, bootstrap likelihood -137248.253843, best rearrangement setting 5 Bootstrap[12]: Time 7.513872 seconds, bootstrap likelihood -137024.070980, best rearrangement setting 8 Bootstrap[13]: Time 7.388911 seconds, bootstrap likelihood -139709.391188, best rearrangement setting 7 Bootstrap[14]: Time 6.989850 seconds, bootstrap likelihood -137570.198198, best rearrangement setting 12 Bootstrap[15]: Time 7.315849 seconds, bootstrap likelihood -137244.356293, best rearrangement setting 15 Bootstrap[16]: Time 7.494789 seconds, bootstrap likelihood -137886.444968, best rearrangement setting 12 Bootstrap[17]: Time 17.856527 seconds, bootstrap likelihood -138197.458262, best rearrangement setting 12 Bootstrap[18]: Time 17.753731 seconds, bootstrap likelihood -136782.586355, best rearrangement setting 5 Bootstrap[19]: Time 17.345987 seconds, bootstrap likelihood -139355.900452, best rearrangement setting 8 Bootstrap[20]: Time 16.975049 seconds, bootstrap likelihood -138455.606397, best rearrangement setting 10 Bootstrap[21]: Time 7.547622 seconds, bootstrap likelihood -137698.429116, best rearrangement setting 6 Bootstrap[22]: Time 16.820789 seconds, bootstrap likelihood -137880.627908, best rearrangement setting 5 Bootstrap[23]: Time 17.252270 seconds, bootstrap likelihood -138140.395237, best rearrangement setting 7 Bootstrap[24]: Time 17.385938 seconds, bootstrap likelihood -137386.224402, best rearrangement setting 8 Bootstrap[25]: Time 18.336977 seconds, bootstrap likelihood -138061.885545, best rearrangement setting 6 Bootstrap[26]: Time 18.463335 seconds, bootstrap likelihood -137237.937298, best rearrangement setting 12 Bootstrap[27]: Time 17.621034 seconds, bootstrap likelihood -137313.191979, best rearrangement setting 10 Bootstrap[28]: Time 7.569038 seconds, bootstrap likelihood -138035.931860, best rearrangement setting 11 Bootstrap[29]: Time 18.394923 seconds, bootstrap likelihood -137239.221254, best rearrangement setting 12 Bootstrap[30]: Time 8.074551 seconds, bootstrap likelihood -136737.260635, best rearrangement setting 15 Bootstrap[31]: Time 16.496587 seconds, bootstrap likelihood -138534.893785, best rearrangement setting 15 Bootstrap[32]: Time 16.827833 seconds, bootstrap likelihood -136523.498646, best rearrangement setting 6 Bootstrap[33]: Time 17.111664 seconds, bootstrap likelihood -137577.851081, best rearrangement setting 15 Bootstrap[34]: Time 7.440507 seconds, bootstrap likelihood -137815.290524, best rearrangement setting 11 Bootstrap[35]: Time 16.635231 seconds, bootstrap likelihood -136920.587193, best rearrangement setting 8 Bootstrap[36]: Time 17.178703 seconds, bootstrap likelihood -135977.231461, best rearrangement setting 9 Bootstrap[37]: Time 8.051466 seconds, bootstrap likelihood -136810.014976, best rearrangement setting 11 Bootstrap[38]: Time 16.801925 seconds, bootstrap likelihood -137022.447024, best rearrangement setting 8 Bootstrap[39]: Time 16.880317 seconds, bootstrap likelihood -136575.013643, best rearrangement setting 13 Bootstrap[40]: Time 7.142556 seconds, bootstrap likelihood -137663.564297, best rearrangement setting 13 Bootstrap[41]: Time 17.905352 seconds, bootstrap likelihood -137295.299680, best rearrangement setting 10 Bootstrap[42]: Time 16.028874 seconds, bootstrap likelihood -137841.906226, best rearrangement setting 5 Bootstrap[43]: Time 18.857680 seconds, bootstrap likelihood -138869.121298, best rearrangement setting 14 Bootstrap[44]: Time 18.781107 seconds, bootstrap likelihood -138624.126002, best rearrangement setting 10 Bootstrap[45]: Time 16.342792 seconds, bootstrap likelihood -136709.836825, best rearrangement setting 15 Bootstrap[46]: Time 16.859171 seconds, bootstrap likelihood -137201.192023, best rearrangement setting 14 Bootstrap[47]: Time 18.665060 seconds, bootstrap likelihood -137616.009910, best rearrangement setting 8 Bootstrap[48]: Time 18.686405 seconds, bootstrap likelihood -138027.316931, best rearrangement setting 6 Bootstrap[49]: Time 18.324883 seconds, bootstrap likelihood -137630.153853, best rearrangement setting 7 Bootstrap[50]: Time 7.706454 seconds, bootstrap likelihood -136911.145169, best rearrangement setting 7 Bootstrap[51]: Time 15.941205 seconds, bootstrap likelihood -136692.257129, best rearrangement setting 11 Bootstrap[52]: Time 15.982763 seconds, bootstrap likelihood -137674.323031, best rearrangement setting 12 Bootstrap[53]: Time 18.653876 seconds, bootstrap likelihood -138939.240172, best rearrangement setting 8 Bootstrap[54]: Time 17.750914 seconds, bootstrap likelihood -137995.640009, best rearrangement setting 9 Bootstrap[55]: Time 18.279157 seconds, bootstrap likelihood -137247.714699, best rearrangement setting 11 Bootstrap[56]: Time 18.881551 seconds, bootstrap likelihood -139081.623447, best rearrangement setting 5 Bootstrap[57]: Time 18.376035 seconds, bootstrap likelihood -136510.651848, best rearrangement setting 7 Bootstrap[58]: Time 17.229403 seconds, bootstrap likelihood -138817.349273, best rearrangement setting 10 Bootstrap[59]: Time 17.774813 seconds, bootstrap likelihood -138681.395938, best rearrangement setting 9 Bootstrap[60]: Time 19.049942 seconds, bootstrap likelihood -137547.592867, best rearrangement setting 7 Bootstrap[61]: Time 17.470516 seconds, bootstrap likelihood -136694.497285, best rearrangement setting 5 Bootstrap[62]: Time 16.919101 seconds, bootstrap likelihood -136180.799210, best rearrangement setting 11 Bootstrap[63]: Time 16.667403 seconds, bootstrap likelihood -138631.730306, best rearrangement setting 12 Bootstrap[64]: Time 17.952196 seconds, bootstrap likelihood -137707.801216, best rearrangement setting 7 Bootstrap[65]: Time 18.147193 seconds, bootstrap likelihood -138301.163582, best rearrangement setting 5 Bootstrap[66]: Time 17.851363 seconds, bootstrap likelihood -137066.290159, best rearrangement setting 5 Bootstrap[67]: Time 18.301617 seconds, bootstrap likelihood -137275.515479, best rearrangement setting 15 Bootstrap[68]: Time 18.355409 seconds, bootstrap likelihood -137080.054337, best rearrangement setting 11 Bootstrap[69]: Time 15.930264 seconds, bootstrap likelihood -135717.483569, best rearrangement setting 5 Bootstrap[70]: Time 17.929089 seconds, bootstrap likelihood -137353.523027, best rearrangement setting 8 Bootstrap[71]: Time 18.230623 seconds, bootstrap likelihood -138200.441759, best rearrangement setting 10 Bootstrap[72]: Time 16.871373 seconds, bootstrap likelihood -138506.872015, best rearrangement setting 11 Bootstrap[73]: Time 17.974702 seconds, bootstrap likelihood -137058.421078, best rearrangement setting 9 Bootstrap[74]: Time 17.660549 seconds, bootstrap likelihood -136501.200040, best rearrangement setting 5 Bootstrap[75]: Time 7.126476 seconds, bootstrap likelihood -137561.494547, best rearrangement setting 8 Bootstrap[76]: Time 7.105816 seconds, bootstrap likelihood -136420.674137, best rearrangement setting 9 Bootstrap[77]: Time 17.904866 seconds, bootstrap likelihood -137950.656792, best rearrangement setting 11 Bootstrap[78]: Time 18.067083 seconds, bootstrap likelihood -137659.754408, best rearrangement setting 15 Bootstrap[79]: Time 7.480149 seconds, bootstrap likelihood -137818.064049, best rearrangement setting 9 Bootstrap[80]: Time 17.911030 seconds, bootstrap likelihood -139375.714279, best rearrangement setting 15 Bootstrap[81]: Time 16.700895 seconds, bootstrap likelihood -138374.961953, best rearrangement setting 7 Bootstrap[82]: Time 7.827424 seconds, bootstrap likelihood -137340.849627, best rearrangement setting 6 Bootstrap[83]: Time 17.298870 seconds, bootstrap likelihood -139096.297946, best rearrangement setting 10 Bootstrap[84]: Time 17.407830 seconds, bootstrap likelihood -136374.905324, best rearrangement setting 11 Bootstrap[85]: Time 17.771571 seconds, bootstrap likelihood -137164.840326, best rearrangement setting 8 Bootstrap[86]: Time 17.445453 seconds, bootstrap likelihood -136840.195494, best rearrangement setting 7 Bootstrap[87]: Time 16.443815 seconds, bootstrap likelihood -135742.667783, best rearrangement setting 7 Bootstrap[88]: Time 17.606874 seconds, bootstrap likelihood -136660.186630, best rearrangement setting 12 Bootstrap[89]: Time 17.282081 seconds, bootstrap likelihood -136736.826598, best rearrangement setting 10 Bootstrap[90]: Time 7.681349 seconds, bootstrap likelihood -135978.220538, best rearrangement setting 8 Bootstrap[91]: Time 17.330784 seconds, bootstrap likelihood -137958.473461, best rearrangement setting 12 Bootstrap[92]: Time 16.651601 seconds, bootstrap likelihood -137208.804825, best rearrangement setting 13 Bootstrap[93]: Time 17.306866 seconds, bootstrap likelihood -137861.799595, best rearrangement setting 15 Bootstrap[94]: Time 17.588775 seconds, bootstrap likelihood -136437.828544, best rearrangement setting 5 Bootstrap[95]: Time 6.491008 seconds, bootstrap likelihood -138012.180630, best rearrangement setting 5 Bootstrap[96]: Time 17.779006 seconds, bootstrap likelihood -137330.730521, best rearrangement setting 13 Bootstrap[97]: Time 17.678242 seconds, bootstrap likelihood -137522.726609, best rearrangement setting 11 Bootstrap[98]: Time 7.369367 seconds, bootstrap likelihood -136771.736905, best rearrangement setting 6 Bootstrap[99]: Time 16.502548 seconds, bootstrap likelihood -137275.149401, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 1727.432849 seconds Average Time per Rapid Bootstrap 17.274328 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 1827.406622 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 79.442721 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.341406 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.156244 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.018733 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.90perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 1551.331658 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1824.098844 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 79.002673 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.322672 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.154507 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.018639 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.90perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -137545.297677 Slow ML Search 1 Likelihood: -137545.297677 Slow ML Search 2 Likelihood: -137545.297677 Slow ML Search 3 Likelihood: -137545.297678 Slow ML Search 4 Likelihood: -137545.297677 Slow ML Search 5 Likelihood: -137545.297677 Slow ML Search 6 Likelihood: -137545.297677 Slow ML Search 7 Likelihood: -137545.297677 Slow ML Search 8 Likelihood: -137545.297677 Slow ML Search 9 Likelihood: -137545.297678 Slow ML optimization finished Slow ML search Time: 987.888657 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1824.276316 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 79.277508 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.332642 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.154544 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.018500 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.90perc_cov_Partition_No Name Provided Thorough ML search Time: 418.206251 seconds Final ML Optimization Likelihood: -137545.293972 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.618984 Tree-Length: 6.078419 rate A <-> R: 0.375289 rate A <-> N: 0.568255 rate A <-> D: 2.109625 rate A <-> C: 4.881014 rate A <-> Q: 0.032041 rate A <-> E: 2.737475 rate A <-> G: 5.501250 rate A <-> H: 0.137822 rate A <-> I: 1.812474 rate A <-> L: 1.187916 rate A <-> K: 0.128580 rate A <-> M: 1.461196 rate A <-> F: 1.074826 rate A <-> P: 4.170420 rate A <-> S: 22.751029 rate A <-> T: 14.672010 rate A <-> W: 0.200074 rate A <-> Y: 0.000000 rate A <-> V: 14.504431 rate R <-> N: 0.255512 rate R <-> D: 0.000000 rate R <-> C: 0.651767 rate R <-> Q: 5.623121 rate R <-> E: 0.692619 rate R <-> G: 1.156105 rate R <-> H: 3.330939 rate R <-> I: 0.248631 rate R <-> L: 0.439686 rate R <-> K: 23.079468 rate R <-> M: 0.875806 rate R <-> F: 0.124134 rate R <-> P: 0.207838 rate R <-> S: 1.322336 rate R <-> T: 0.579378 rate R <-> W: 0.749704 rate R <-> Y: 0.213651 rate R <-> V: 0.000000 rate N <-> D: 14.411557 rate N <-> C: 0.997275 rate N <-> Q: 7.372276 rate N <-> E: 3.544619 rate N <-> G: 2.370369 rate N <-> H: 8.567897 rate N <-> I: 2.583483 rate N <-> L: 0.935206 rate N <-> K: 8.493952 rate N <-> M: 0.735444 rate N <-> F: 0.591258 rate N <-> P: 0.404737 rate N <-> S: 15.054388 rate N <-> T: 8.918362 rate N <-> W: 0.269467 rate N <-> Y: 3.957612 rate N <-> V: 0.304430 rate D <-> C: 0.757060 rate D <-> Q: 0.000000 rate D <-> E: 31.990212 rate D <-> G: 2.434379 rate D <-> H: 1.731679 rate D <-> I: 0.095784 rate D <-> L: 0.091083 rate D <-> K: 0.826016 rate D <-> M: 0.016329 rate D <-> F: 0.079694 rate D <-> P: 0.928238 rate D <-> S: 3.453779 rate D <-> T: 1.076542 rate D <-> W: 0.206596 rate D <-> Y: 0.641797 rate D <-> V: 0.390832 rate C <-> Q: 0.000000 rate C <-> E: 0.132279 rate C <-> G: 2.659420 rate C <-> H: 3.514492 rate C <-> I: 1.158188 rate C <-> L: 1.328529 rate C <-> K: 0.000000 rate C <-> M: 2.737574 rate C <-> F: 1.744399 rate C <-> P: 0.000000 rate C <-> S: 10.519993 rate C <-> T: 2.915776 rate C <-> W: 0.878993 rate C <-> Y: 4.919958 rate C <-> V: 4.396900 rate Q <-> E: 7.859862 rate Q <-> G: 0.000000 rate Q <-> H: 19.522477 rate Q <-> I: 0.568561 rate Q <-> L: 1.678026 rate Q <-> K: 6.798396 rate Q <-> M: 2.082735 rate Q <-> F: 0.292307 rate Q <-> P: 3.016188 rate Q <-> S: 2.146104 rate Q <-> T: 1.851978 rate Q <-> W: 0.000000 rate Q <-> Y: 1.326809 rate Q <-> V: 0.000000 rate E <-> G: 2.142184 rate E <-> H: 0.091306 rate E <-> I: 0.259264 rate E <-> L: 0.423608 rate E <-> K: 4.040599 rate E <-> M: 0.000000 rate E <-> F: 0.135705 rate E <-> P: 0.384632 rate E <-> S: 2.363710 rate E <-> T: 1.601513 rate E <-> W: 0.162876 rate E <-> Y: 0.717063 rate E <-> V: 0.694683 rate G <-> H: 0.699254 rate G <-> I: 0.127098 rate G <-> L: 0.029649 rate G <-> K: 0.342013 rate G <-> M: 0.092303 rate G <-> F: 0.275145 rate G <-> P: 0.132639 rate G <-> S: 6.163740 rate G <-> T: 0.410876 rate G <-> W: 0.559444 rate G <-> Y: 0.000000 rate G <-> V: 0.674279 rate H <-> I: 0.208770 rate H <-> L: 0.751495 rate H <-> K: 0.348903 rate H <-> M: 0.000000 rate H <-> F: 0.668033 rate H <-> P: 0.317963 rate H <-> S: 1.734863 rate H <-> T: 1.238844 rate H <-> W: 0.000000 rate H <-> Y: 12.421568 rate H <-> V: 0.000000 rate I <-> L: 17.665744 rate I <-> K: 1.316668 rate I <-> M: 16.014469 rate I <-> F: 3.329621 rate I <-> P: 0.072416 rate I <-> S: 1.223477 rate I <-> T: 8.750769 rate I <-> W: 0.485035 rate I <-> Y: 2.398644 rate I <-> V: 50.019170 rate L <-> K: 0.565161 rate L <-> M: 13.132105 rate L <-> F: 6.193212 rate L <-> P: 1.059255 rate L <-> S: 1.712209 rate L <-> T: 1.596892 rate L <-> W: 1.255977 rate L <-> Y: 1.320702 rate L <-> V: 5.037220 rate K <-> M: 0.610530 rate K <-> F: 0.130198 rate K <-> P: 0.374547 rate K <-> S: 2.004165 rate K <-> T: 1.821073 rate K <-> W: 0.152385 rate K <-> Y: 0.806083 rate K <-> V: 0.250921 rate M <-> F: 1.281051 rate M <-> P: 0.133209 rate M <-> S: 0.649654 rate M <-> T: 5.951097 rate M <-> W: 0.424258 rate M <-> Y: 0.815553 rate M <-> V: 7.283043 rate F <-> P: 0.153046 rate F <-> S: 1.324217 rate F <-> T: 0.584529 rate F <-> W: 0.917605 rate F <-> Y: 10.627690 rate F <-> V: 1.366470 rate P <-> S: 6.048992 rate P <-> T: 3.300844 rate P <-> W: 0.476430 rate P <-> Y: 0.907087 rate P <-> V: 1.020563 rate S <-> T: 21.541048 rate S <-> W: 0.229742 rate S <-> Y: 1.517977 rate S <-> V: 1.286508 rate T <-> W: 0.000000 rate T <-> Y: 0.927146 rate T <-> V: 12.336817 rate W <-> Y: 1.852842 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.042615 freq pi(R): 0.037103 freq pi(N): 0.065104 freq pi(D): 0.027146 freq pi(C): 0.012643 freq pi(Q): 0.016929 freq pi(E): 0.032827 freq pi(G): 0.039520 freq pi(H): 0.016887 freq pi(I): 0.076136 freq pi(L): 0.123295 freq pi(K): 0.081218 freq pi(M): 0.017689 freq pi(F): 0.144000 freq pi(P): 0.020561 freq pi(S): 0.074616 freq pi(T): 0.045614 freq pi(W): 0.015597 freq pi(Y): 0.054904 freq pi(V): 0.055598 ML search took 2957.513494 secs or 0.821532 hours Combined Bootstrap and ML search took 4684.950630 secs or 1.301375 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.90perc_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.90perc_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.90perc_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.90perc_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.90perc_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.90perc_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.90perc_cov Overall execution time for full ML analysis: 4685.057654 secs or 1.301405 hours or 0.054225 days