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 7781 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 13.57% 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: 7781 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.80perc_cov.fa -n RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.80perc_cov -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 1941.640496 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 89.576379 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.048846 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.80perc_cov_Partition_No Name Provided Time for BS model parameter optimization 214.215171 Bootstrap[0]: Time 235.135477 seconds, bootstrap likelihood -146233.924585, best rearrangement setting 13 Bootstrap[1]: Time 7.931121 seconds, bootstrap likelihood -145798.169524, best rearrangement setting 13 Bootstrap[2]: Time 20.062237 seconds, bootstrap likelihood -148064.185590, best rearrangement setting 12 Bootstrap[3]: Time 18.534474 seconds, bootstrap likelihood -148643.651019, best rearrangement setting 15 Bootstrap[4]: Time 7.284074 seconds, bootstrap likelihood -147738.849053, best rearrangement setting 10 Bootstrap[5]: Time 16.955523 seconds, bootstrap likelihood -147787.841822, best rearrangement setting 10 Bootstrap[6]: Time 18.577260 seconds, bootstrap likelihood -148121.740673, best rearrangement setting 6 Bootstrap[7]: Time 18.372081 seconds, bootstrap likelihood -148976.872464, best rearrangement setting 14 Bootstrap[8]: Time 19.124185 seconds, bootstrap likelihood -145661.298189, best rearrangement setting 5 Bootstrap[9]: Time 18.461327 seconds, bootstrap likelihood -147420.277131, best rearrangement setting 7 Bootstrap[10]: Time 20.393762 seconds, bootstrap likelihood -148964.941683, best rearrangement setting 7 Bootstrap[11]: Time 18.424162 seconds, bootstrap likelihood -149165.366593, best rearrangement setting 5 Bootstrap[12]: Time 18.278866 seconds, bootstrap likelihood -146929.805390, best rearrangement setting 8 Bootstrap[13]: Time 8.452250 seconds, bootstrap likelihood -147851.839562, best rearrangement setting 7 Bootstrap[14]: Time 18.795560 seconds, bootstrap likelihood -146717.902070, best rearrangement setting 12 Bootstrap[15]: Time 18.817181 seconds, bootstrap likelihood -148131.155365, best rearrangement setting 15 Bootstrap[16]: Time 19.293829 seconds, bootstrap likelihood -148095.583801, best rearrangement setting 12 Bootstrap[17]: Time 19.441895 seconds, bootstrap likelihood -148249.903018, best rearrangement setting 12 Bootstrap[18]: Time 18.677768 seconds, bootstrap likelihood -148254.700079, best rearrangement setting 5 Bootstrap[19]: Time 19.276940 seconds, bootstrap likelihood -148371.564012, best rearrangement setting 8 Bootstrap[20]: Time 20.474809 seconds, bootstrap likelihood -146933.102679, best rearrangement setting 10 Bootstrap[21]: Time 17.410012 seconds, bootstrap likelihood -148363.391171, best rearrangement setting 6 Bootstrap[22]: Time 19.927628 seconds, bootstrap likelihood -147173.387027, best rearrangement setting 5 Bootstrap[23]: Time 18.705268 seconds, bootstrap likelihood -147045.306793, best rearrangement setting 7 Bootstrap[24]: Time 18.109741 seconds, bootstrap likelihood -147503.017367, best rearrangement setting 8 Bootstrap[25]: Time 18.875255 seconds, bootstrap likelihood -148612.898816, best rearrangement setting 6 Bootstrap[26]: Time 19.801959 seconds, bootstrap likelihood -145751.330291, best rearrangement setting 12 Bootstrap[27]: Time 20.111183 seconds, bootstrap likelihood -147158.340903, best rearrangement setting 10 Bootstrap[28]: Time 20.260147 seconds, bootstrap likelihood -146823.132766, best rearrangement setting 11 Bootstrap[29]: Time 19.694768 seconds, bootstrap likelihood -148655.816412, best rearrangement setting 12 Bootstrap[30]: Time 19.930639 seconds, bootstrap likelihood -147254.269299, best rearrangement setting 15 Bootstrap[31]: Time 20.836806 seconds, bootstrap likelihood -148729.981895, best rearrangement setting 15 Bootstrap[32]: Time 20.226597 seconds, bootstrap likelihood -147476.259524, best rearrangement setting 6 Bootstrap[33]: Time 18.744872 seconds, bootstrap likelihood -146929.500875, best rearrangement setting 15 Bootstrap[34]: Time 19.369987 seconds, bootstrap likelihood -148392.006764, best rearrangement setting 11 Bootstrap[35]: Time 19.349000 seconds, bootstrap likelihood -146668.648293, best rearrangement setting 8 Bootstrap[36]: Time 19.337308 seconds, bootstrap likelihood -148012.051456, best rearrangement setting 9 Bootstrap[37]: Time 19.519649 seconds, bootstrap likelihood -146936.180056, best rearrangement setting 11 Bootstrap[38]: Time 20.085272 seconds, bootstrap likelihood -148650.861069, best rearrangement setting 8 Bootstrap[39]: Time 19.934484 seconds, bootstrap likelihood -145394.451224, best rearrangement setting 13 Bootstrap[40]: Time 7.513117 seconds, bootstrap likelihood -147672.090179, best rearrangement setting 13 Bootstrap[41]: Time 19.785440 seconds, bootstrap likelihood -148657.175509, best rearrangement setting 10 Bootstrap[42]: Time 18.716449 seconds, bootstrap likelihood -148599.406297, best rearrangement setting 5 Bootstrap[43]: Time 18.468910 seconds, bootstrap likelihood -147553.448939, best rearrangement setting 14 Bootstrap[44]: Time 18.508879 seconds, bootstrap likelihood -145089.267938, best rearrangement setting 10 Bootstrap[45]: Time 19.156685 seconds, bootstrap likelihood -148530.228703, best rearrangement setting 15 Bootstrap[46]: Time 20.203958 seconds, bootstrap likelihood -148559.283979, best rearrangement setting 14 Bootstrap[47]: Time 19.775887 seconds, bootstrap likelihood -146596.452033, best rearrangement setting 8 Bootstrap[48]: Time 19.178538 seconds, bootstrap likelihood -146180.945545, best rearrangement setting 6 Bootstrap[49]: Time 19.400644 seconds, bootstrap likelihood -147721.271476, best rearrangement setting 7 Bootstrap[50]: Time 19.706910 seconds, bootstrap likelihood -147768.389170, best rearrangement setting 7 Bootstrap[51]: Time 18.954199 seconds, bootstrap likelihood -147762.646361, best rearrangement setting 11 Bootstrap[52]: Time 19.933281 seconds, bootstrap likelihood -145859.388926, best rearrangement setting 12 Bootstrap[53]: Time 18.067010 seconds, bootstrap likelihood -147437.679936, best rearrangement setting 8 Bootstrap[54]: Time 18.353644 seconds, bootstrap likelihood -147577.445707, best rearrangement setting 9 Bootstrap[55]: Time 19.691061 seconds, bootstrap likelihood -148590.069838, best rearrangement setting 11 Bootstrap[56]: Time 19.785422 seconds, bootstrap likelihood -149168.216900, best rearrangement setting 5 Bootstrap[57]: Time 18.595396 seconds, bootstrap likelihood -146639.448829, best rearrangement setting 7 Bootstrap[58]: Time 19.816838 seconds, bootstrap likelihood -145724.214438, best rearrangement setting 10 Bootstrap[59]: Time 20.224109 seconds, bootstrap likelihood -147768.960400, best rearrangement setting 9 Bootstrap[60]: Time 20.064098 seconds, bootstrap likelihood -148995.105390, best rearrangement setting 7 Bootstrap[61]: Time 19.048469 seconds, bootstrap likelihood -147581.659966, best rearrangement setting 5 Bootstrap[62]: Time 18.899918 seconds, bootstrap likelihood -147695.564204, best rearrangement setting 11 Bootstrap[63]: Time 20.383578 seconds, bootstrap likelihood -149718.913377, best rearrangement setting 12 Bootstrap[64]: Time 17.828955 seconds, bootstrap likelihood -148535.656709, best rearrangement setting 7 Bootstrap[65]: Time 18.953840 seconds, bootstrap likelihood -145680.564389, best rearrangement setting 5 Bootstrap[66]: Time 19.612209 seconds, bootstrap likelihood -146656.734037, best rearrangement setting 5 Bootstrap[67]: Time 20.641733 seconds, bootstrap likelihood -146819.277109, best rearrangement setting 15 Bootstrap[68]: Time 21.050595 seconds, bootstrap likelihood -147702.395940, best rearrangement setting 11 Bootstrap[69]: Time 18.055049 seconds, bootstrap likelihood -147610.053630, best rearrangement setting 5 Bootstrap[70]: Time 19.750997 seconds, bootstrap likelihood -145921.470035, best rearrangement setting 8 Bootstrap[71]: Time 19.671617 seconds, bootstrap likelihood -146660.602603, best rearrangement setting 10 Bootstrap[72]: Time 18.841091 seconds, bootstrap likelihood -147675.073473, best rearrangement setting 11 Bootstrap[73]: Time 18.787567 seconds, bootstrap likelihood -147559.141916, best rearrangement setting 9 Bootstrap[74]: Time 20.104762 seconds, bootstrap likelihood -147727.488029, best rearrangement setting 5 Bootstrap[75]: Time 18.581577 seconds, bootstrap likelihood -147734.838421, best rearrangement setting 8 Bootstrap[76]: Time 18.713191 seconds, bootstrap likelihood -146626.554192, best rearrangement setting 9 Bootstrap[77]: Time 18.341091 seconds, bootstrap likelihood -147658.493767, best rearrangement setting 11 Bootstrap[78]: Time 20.056900 seconds, bootstrap likelihood -147185.981832, best rearrangement setting 15 Bootstrap[79]: Time 19.911011 seconds, bootstrap likelihood -147084.180160, best rearrangement setting 9 Bootstrap[80]: Time 19.917552 seconds, bootstrap likelihood -147238.219794, best rearrangement setting 15 Bootstrap[81]: Time 18.324256 seconds, bootstrap likelihood -146849.342392, best rearrangement setting 7 Bootstrap[82]: Time 19.722580 seconds, bootstrap likelihood -146707.783252, best rearrangement setting 6 Bootstrap[83]: Time 17.672331 seconds, bootstrap likelihood -146184.062749, best rearrangement setting 10 Bootstrap[84]: Time 19.979018 seconds, bootstrap likelihood -147886.725739, best rearrangement setting 11 Bootstrap[85]: Time 19.526958 seconds, bootstrap likelihood -146402.423609, best rearrangement setting 8 Bootstrap[86]: Time 18.472021 seconds, bootstrap likelihood -146558.639298, best rearrangement setting 7 Bootstrap[87]: Time 19.182799 seconds, bootstrap likelihood -147650.058763, best rearrangement setting 7 Bootstrap[88]: Time 19.202558 seconds, bootstrap likelihood -147035.455093, best rearrangement setting 12 Bootstrap[89]: Time 19.100036 seconds, bootstrap likelihood -147675.776016, best rearrangement setting 10 Bootstrap[90]: Time 19.786217 seconds, bootstrap likelihood -148146.556511, best rearrangement setting 8 Bootstrap[91]: Time 17.586448 seconds, bootstrap likelihood -149185.672815, best rearrangement setting 12 Bootstrap[92]: Time 19.821168 seconds, bootstrap likelihood -147029.626923, best rearrangement setting 13 Bootstrap[93]: Time 19.678369 seconds, bootstrap likelihood -146776.721677, best rearrangement setting 15 Bootstrap[94]: Time 19.571353 seconds, bootstrap likelihood -145925.244242, best rearrangement setting 5 Bootstrap[95]: Time 18.554325 seconds, bootstrap likelihood -147633.514454, best rearrangement setting 5 Bootstrap[96]: Time 18.987963 seconds, bootstrap likelihood -148677.297354, best rearrangement setting 13 Bootstrap[97]: Time 8.574383 seconds, bootstrap likelihood -147614.267130, best rearrangement setting 11 Bootstrap[98]: Time 19.169500 seconds, bootstrap likelihood -148447.858882, best rearrangement setting 6 Bootstrap[99]: Time 19.441350 seconds, bootstrap likelihood -146838.792668, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 2084.881800 seconds Average Time per Rapid Bootstrap 20.848818 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 1949.895389 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 89.546722 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.119959 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.221638 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.025098 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.80perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 1885.319991 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1942.550747 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 89.277767 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.029294 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.215951 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.025579 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.80perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -147601.600197 Slow ML Search 1 Likelihood: -147601.600197 Slow ML Search 2 Likelihood: -147601.600196 Slow ML Search 3 Likelihood: -147601.600197 Slow ML Search 4 Likelihood: -147601.600197 Slow ML Search 5 Likelihood: -147601.600197 Slow ML Search 6 Likelihood: -147601.600197 Slow ML Search 7 Likelihood: -147601.600196 Slow ML Search 8 Likelihood: -147601.600196 Slow ML Search 9 Likelihood: -147601.600196 Slow ML optimization finished Slow ML search Time: 1091.397280 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1942.719908 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 89.593608 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.038198 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.213284 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.024944 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.80perc_cov_Partition_No Name Provided Thorough ML search Time: 448.902088 seconds Final ML Optimization Likelihood: -147601.598297 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.602313 Tree-Length: 6.608370 rate A <-> R: 0.332256 rate A <-> N: 0.529360 rate A <-> D: 2.966632 rate A <-> C: 4.769047 rate A <-> Q: 0.266942 rate A <-> E: 2.976481 rate A <-> G: 6.116235 rate A <-> H: 0.203206 rate A <-> I: 1.809028 rate A <-> L: 1.228791 rate A <-> K: 0.247392 rate A <-> M: 1.340098 rate A <-> F: 1.043489 rate A <-> P: 4.490038 rate A <-> S: 22.851357 rate A <-> T: 15.772080 rate A <-> W: 0.183379 rate A <-> Y: 0.072572 rate A <-> V: 14.714390 rate R <-> N: 0.169014 rate R <-> D: 0.000000 rate R <-> C: 0.977274 rate R <-> Q: 5.917533 rate R <-> E: 0.893982 rate R <-> G: 1.298218 rate R <-> H: 3.555769 rate R <-> I: 0.205618 rate R <-> L: 0.487706 rate R <-> K: 22.252550 rate R <-> M: 0.836796 rate R <-> F: 0.140192 rate R <-> P: 0.187170 rate R <-> S: 1.304841 rate R <-> T: 0.614301 rate R <-> W: 0.759979 rate R <-> Y: 0.270537 rate R <-> V: 0.000000 rate N <-> D: 14.496700 rate N <-> C: 1.066915 rate N <-> Q: 7.069757 rate N <-> E: 3.289309 rate N <-> G: 2.371403 rate N <-> H: 8.424761 rate N <-> I: 2.592206 rate N <-> L: 0.915975 rate N <-> K: 8.528750 rate N <-> M: 0.688942 rate N <-> F: 0.584515 rate N <-> P: 0.404805 rate N <-> S: 15.169196 rate N <-> T: 8.820403 rate N <-> W: 0.249703 rate N <-> Y: 3.719155 rate N <-> V: 0.257892 rate D <-> C: 0.903290 rate D <-> Q: 0.000000 rate D <-> E: 32.357929 rate D <-> G: 2.771940 rate D <-> H: 1.752555 rate D <-> I: 0.110635 rate D <-> L: 0.219303 rate D <-> K: 1.122115 rate D <-> M: 0.000000 rate D <-> F: 0.078670 rate D <-> P: 0.720269 rate D <-> S: 3.599709 rate D <-> T: 1.527999 rate D <-> W: 0.208008 rate D <-> Y: 0.583904 rate D <-> V: 0.300495 rate C <-> Q: 0.000000 rate C <-> E: 0.018177 rate C <-> G: 3.364044 rate C <-> H: 3.321767 rate C <-> I: 1.053748 rate C <-> L: 1.339724 rate C <-> K: 0.000000 rate C <-> M: 2.527262 rate C <-> F: 1.700192 rate C <-> P: 0.000000 rate C <-> S: 10.171110 rate C <-> T: 2.742217 rate C <-> W: 0.838481 rate C <-> Y: 5.120638 rate C <-> V: 4.408410 rate Q <-> E: 8.632197 rate Q <-> G: 0.000000 rate Q <-> H: 23.195810 rate Q <-> I: 0.616661 rate Q <-> L: 1.644280 rate Q <-> K: 7.255126 rate Q <-> M: 2.034137 rate Q <-> F: 0.282147 rate Q <-> P: 3.162278 rate Q <-> S: 2.099080 rate Q <-> T: 1.569137 rate Q <-> W: 0.000000 rate Q <-> Y: 1.708512 rate Q <-> V: 0.000000 rate E <-> G: 3.356916 rate E <-> H: 0.727295 rate E <-> I: 0.209608 rate E <-> L: 0.433320 rate E <-> K: 4.030287 rate E <-> M: 0.000000 rate E <-> F: 0.095752 rate E <-> P: 0.901897 rate E <-> S: 2.418856 rate E <-> T: 1.824094 rate E <-> W: 0.188849 rate E <-> Y: 0.661431 rate E <-> V: 1.016162 rate G <-> H: 0.678003 rate G <-> I: 0.133293 rate G <-> L: 0.042091 rate G <-> K: 0.291671 rate G <-> M: 0.123562 rate G <-> F: 0.295658 rate G <-> P: 0.125354 rate G <-> S: 6.749209 rate G <-> T: 0.596326 rate G <-> W: 0.677416 rate G <-> Y: 0.000000 rate G <-> V: 0.753509 rate H <-> I: 0.345693 rate H <-> L: 0.723626 rate H <-> K: 0.378313 rate H <-> M: 0.000000 rate H <-> F: 0.647627 rate H <-> P: 1.009391 rate H <-> S: 1.693510 rate H <-> T: 1.557175 rate H <-> W: 0.000000 rate H <-> Y: 13.065681 rate H <-> V: 0.000000 rate I <-> L: 17.367519 rate I <-> K: 1.353414 rate I <-> M: 16.515043 rate I <-> F: 3.317034 rate I <-> P: 0.059043 rate I <-> S: 1.184822 rate I <-> T: 8.960857 rate I <-> W: 0.446306 rate I <-> Y: 2.331087 rate I <-> V: 49.636027 rate L <-> K: 0.594032 rate L <-> M: 13.149635 rate L <-> F: 6.095102 rate L <-> P: 1.122624 rate L <-> S: 1.722442 rate L <-> T: 1.787023 rate L <-> W: 1.234473 rate L <-> Y: 1.288662 rate L <-> V: 4.842791 rate K <-> M: 0.599548 rate K <-> F: 0.123256 rate K <-> P: 0.356804 rate K <-> S: 2.035712 rate K <-> T: 1.903965 rate K <-> W: 0.187744 rate K <-> Y: 0.785088 rate K <-> V: 0.303874 rate M <-> F: 1.255477 rate M <-> P: 0.093076 rate M <-> S: 0.634165 rate M <-> T: 5.958089 rate M <-> W: 0.408336 rate M <-> Y: 0.736979 rate M <-> V: 7.302561 rate F <-> P: 0.183626 rate F <-> S: 1.327193 rate F <-> T: 0.608459 rate F <-> W: 1.016647 rate F <-> Y: 10.276478 rate F <-> V: 1.353824 rate P <-> S: 6.169895 rate P <-> T: 3.484077 rate P <-> W: 0.440594 rate P <-> Y: 0.939433 rate P <-> V: 1.270973 rate S <-> T: 21.806843 rate S <-> W: 0.208656 rate S <-> Y: 1.544509 rate S <-> V: 1.390958 rate T <-> W: 0.000000 rate T <-> Y: 0.939747 rate T <-> V: 11.914750 rate W <-> Y: 1.708782 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.042462 freq pi(R): 0.036857 freq pi(N): 0.065339 freq pi(D): 0.028082 freq pi(C): 0.012491 freq pi(Q): 0.017258 freq pi(E): 0.034783 freq pi(G): 0.039187 freq pi(H): 0.016839 freq pi(I): 0.075018 freq pi(L): 0.123558 freq pi(K): 0.082078 freq pi(M): 0.017352 freq pi(F): 0.143328 freq pi(P): 0.021131 freq pi(S): 0.074342 freq pi(T): 0.044868 freq pi(W): 0.015216 freq pi(Y): 0.054578 freq pi(V): 0.055235 ML search took 3425.705028 secs or 0.951585 hours Combined Bootstrap and ML search took 5510.587743 secs or 1.530719 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.80perc_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.80perc_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.80perc_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.80perc_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.80perc_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.80perc_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.80perc_cov Overall execution time for full ML analysis: 5510.675072 secs or 1.530743 hours or 0.063781 days