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 9294 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 18.81% 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 ML estimate of 25 per site rate categories Likelihood of final tree will be evaluated and optimized under GAMMA GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units Partition: 0 Alignment Patterns: 9294 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.80perc_cov.fa -n RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov -m PROTCATGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 13482.006468 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3065.730313 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 162.170508 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.541361 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.295048 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Time for BS model parameter optimization 181.246185 Bootstrap[0]: Time 191.405383 seconds, bootstrap likelihood -159609.522525, best rearrangement setting 13 Bootstrap[1]: Time 2.829833 seconds, bootstrap likelihood -159935.040919, best rearrangement setting 13 Bootstrap[2]: Time 8.956985 seconds, bootstrap likelihood -159660.414351, best rearrangement setting 12 Bootstrap[3]: Time 9.091703 seconds, bootstrap likelihood -159508.223599, best rearrangement setting 15 Bootstrap[4]: Time 8.737767 seconds, bootstrap likelihood -161165.704080, best rearrangement setting 10 Bootstrap[5]: Time 8.829766 seconds, bootstrap likelihood -161468.368013, best rearrangement setting 10 Bootstrap[6]: Time 8.330806 seconds, bootstrap likelihood -160688.816925, best rearrangement setting 6 Bootstrap[7]: Time 8.842006 seconds, bootstrap likelihood -161505.081408, best rearrangement setting 14 Bootstrap[8]: Time 8.050998 seconds, bootstrap likelihood -158928.121902, best rearrangement setting 5 Bootstrap[9]: Time 8.652497 seconds, bootstrap likelihood -160672.871606, best rearrangement setting 7 Bootstrap[10]: Time 3.452075 seconds, bootstrap likelihood -161856.470669, best rearrangement setting 7 Bootstrap[11]: Time 2.949943 seconds, bootstrap likelihood -160060.519492, best rearrangement setting 5 Bootstrap[12]: Time 9.153164 seconds, bootstrap likelihood -163130.042786, best rearrangement setting 8 Bootstrap[13]: Time 9.610196 seconds, bootstrap likelihood -160843.901085, best rearrangement setting 7 Bootstrap[14]: Time 9.489178 seconds, bootstrap likelihood -159605.945340, best rearrangement setting 12 Bootstrap[15]: Time 8.955325 seconds, bootstrap likelihood -161918.303725, best rearrangement setting 15 Bootstrap[16]: Time 8.784128 seconds, bootstrap likelihood -159950.979774, best rearrangement setting 12 Bootstrap[17]: Time 8.609446 seconds, bootstrap likelihood -159838.417274, best rearrangement setting 12 Bootstrap[18]: Time 8.531953 seconds, bootstrap likelihood -161794.378697, best rearrangement setting 5 Bootstrap[19]: Time 8.948062 seconds, bootstrap likelihood -159964.423057, best rearrangement setting 8 Bootstrap[20]: Time 9.658763 seconds, bootstrap likelihood -160237.577744, best rearrangement setting 10 Bootstrap[21]: Time 8.721925 seconds, bootstrap likelihood -161993.906597, best rearrangement setting 6 Bootstrap[22]: Time 2.961119 seconds, bootstrap likelihood -159732.023128, best rearrangement setting 5 Bootstrap[23]: Time 8.743011 seconds, bootstrap likelihood -160303.307583, best rearrangement setting 7 Bootstrap[24]: Time 8.821904 seconds, bootstrap likelihood -160847.183976, best rearrangement setting 8 Bootstrap[25]: Time 8.298785 seconds, bootstrap likelihood -160891.518661, best rearrangement setting 6 Bootstrap[26]: Time 9.117105 seconds, bootstrap likelihood -159889.259164, best rearrangement setting 12 Bootstrap[27]: Time 9.456522 seconds, bootstrap likelihood -159940.203698, best rearrangement setting 10 Bootstrap[28]: Time 8.776866 seconds, bootstrap likelihood -160211.008036, best rearrangement setting 11 Bootstrap[29]: Time 9.226285 seconds, bootstrap likelihood -160600.683676, best rearrangement setting 12 Bootstrap[30]: Time 9.347169 seconds, bootstrap likelihood -160251.159160, best rearrangement setting 15 Bootstrap[31]: Time 8.645421 seconds, bootstrap likelihood -160411.358575, best rearrangement setting 15 Bootstrap[32]: Time 8.657448 seconds, bootstrap likelihood -160075.609812, best rearrangement setting 6 Bootstrap[33]: Time 8.726784 seconds, bootstrap likelihood -160056.989808, best rearrangement setting 15 Bootstrap[34]: Time 9.186449 seconds, bootstrap likelihood -159726.732367, best rearrangement setting 11 Bootstrap[35]: Time 8.735221 seconds, bootstrap likelihood -160384.127013, best rearrangement setting 8 Bootstrap[36]: Time 8.879789 seconds, bootstrap likelihood -159528.887085, best rearrangement setting 9 Bootstrap[37]: Time 8.877372 seconds, bootstrap likelihood -158790.978162, best rearrangement setting 11 Bootstrap[38]: Time 9.552837 seconds, bootstrap likelihood -159144.522178, best rearrangement setting 8 Bootstrap[39]: Time 8.941150 seconds, bootstrap likelihood -159480.808410, best rearrangement setting 13 Bootstrap[40]: Time 10.030963 seconds, bootstrap likelihood -161349.634285, best rearrangement setting 13 Bootstrap[41]: Time 9.690703 seconds, bootstrap likelihood -161106.352170, best rearrangement setting 10 Bootstrap[42]: Time 8.683928 seconds, bootstrap likelihood -160209.386621, best rearrangement setting 5 Bootstrap[43]: Time 8.980649 seconds, bootstrap likelihood -159938.846330, best rearrangement setting 14 Bootstrap[44]: Time 9.038398 seconds, bootstrap likelihood -160588.042691, best rearrangement setting 10 Bootstrap[45]: Time 8.474507 seconds, bootstrap likelihood -161581.891020, best rearrangement setting 15 Bootstrap[46]: Time 8.474885 seconds, bootstrap likelihood -161486.199918, best rearrangement setting 14 Bootstrap[47]: Time 8.990197 seconds, bootstrap likelihood -158308.476705, best rearrangement setting 8 Bootstrap[48]: Time 8.841505 seconds, bootstrap likelihood -160187.736698, best rearrangement setting 6 Bootstrap[49]: Time 8.668252 seconds, bootstrap likelihood -159593.462984, best rearrangement setting 7 Bootstrap[50]: Time 9.230606 seconds, bootstrap likelihood -160621.158336, best rearrangement setting 7 Bootstrap[51]: Time 2.881959 seconds, bootstrap likelihood -159298.770917, best rearrangement setting 11 Bootstrap[52]: Time 9.145184 seconds, bootstrap likelihood -160548.058641, best rearrangement setting 12 Bootstrap[53]: Time 8.600620 seconds, bootstrap likelihood -159187.791144, best rearrangement setting 8 Bootstrap[54]: Time 8.402752 seconds, bootstrap likelihood -160073.724606, best rearrangement setting 9 Bootstrap[55]: Time 2.878422 seconds, bootstrap likelihood -160488.592679, best rearrangement setting 11 Bootstrap[56]: Time 2.873277 seconds, bootstrap likelihood -159214.636201, best rearrangement setting 5 Bootstrap[57]: Time 8.992119 seconds, bootstrap likelihood -159588.655860, best rearrangement setting 7 Bootstrap[58]: Time 9.110697 seconds, bootstrap likelihood -161163.073679, best rearrangement setting 10 Bootstrap[59]: Time 8.837855 seconds, bootstrap likelihood -161444.759609, best rearrangement setting 9 Bootstrap[60]: Time 8.740459 seconds, bootstrap likelihood -161175.410394, best rearrangement setting 7 Bootstrap[61]: Time 8.296133 seconds, bootstrap likelihood -158997.839065, best rearrangement setting 5 Bootstrap[62]: Time 8.691184 seconds, bootstrap likelihood -161468.588786, best rearrangement setting 11 Bootstrap[63]: Time 8.726901 seconds, bootstrap likelihood -160524.815349, best rearrangement setting 12 Bootstrap[64]: Time 8.733790 seconds, bootstrap likelihood -159732.085963, best rearrangement setting 7 Bootstrap[65]: Time 8.927365 seconds, bootstrap likelihood -159681.446855, best rearrangement setting 5 Bootstrap[66]: Time 8.563514 seconds, bootstrap likelihood -160430.248905, best rearrangement setting 5 Bootstrap[67]: Time 8.578874 seconds, bootstrap likelihood -159947.806686, best rearrangement setting 15 Bootstrap[68]: Time 2.977344 seconds, bootstrap likelihood -161223.569997, best rearrangement setting 11 Bootstrap[69]: Time 8.241524 seconds, bootstrap likelihood -158804.355973, best rearrangement setting 5 Bootstrap[70]: Time 9.220009 seconds, bootstrap likelihood -159708.921460, best rearrangement setting 8 Bootstrap[71]: Time 8.545395 seconds, bootstrap likelihood -161410.852957, best rearrangement setting 10 Bootstrap[72]: Time 9.089591 seconds, bootstrap likelihood -162028.709065, best rearrangement setting 11 Bootstrap[73]: Time 8.837337 seconds, bootstrap likelihood -159935.698287, best rearrangement setting 9 Bootstrap[74]: Time 2.959737 seconds, bootstrap likelihood -161743.285940, best rearrangement setting 5 Bootstrap[75]: Time 9.050442 seconds, bootstrap likelihood -161120.995102, best rearrangement setting 8 Bootstrap[76]: Time 9.871183 seconds, bootstrap likelihood -159692.422099, best rearrangement setting 9 Bootstrap[77]: Time 9.441829 seconds, bootstrap likelihood -160749.190082, best rearrangement setting 11 Bootstrap[78]: Time 9.336889 seconds, bootstrap likelihood -161301.812214, best rearrangement setting 15 Bootstrap[79]: Time 2.943466 seconds, bootstrap likelihood -158580.389138, best rearrangement setting 9 Bootstrap[80]: Time 9.154065 seconds, bootstrap likelihood -161125.803375, best rearrangement setting 15 Bootstrap[81]: Time 9.414263 seconds, bootstrap likelihood -158875.633907, best rearrangement setting 7 Bootstrap[82]: Time 9.075103 seconds, bootstrap likelihood -159959.632312, best rearrangement setting 6 Bootstrap[83]: Time 9.101788 seconds, bootstrap likelihood -160908.772630, best rearrangement setting 10 Bootstrap[84]: Time 9.139118 seconds, bootstrap likelihood -159445.811737, best rearrangement setting 11 Bootstrap[85]: Time 9.051663 seconds, bootstrap likelihood -160373.627448, best rearrangement setting 8 Bootstrap[86]: Time 9.022472 seconds, bootstrap likelihood -159606.242496, best rearrangement setting 7 Bootstrap[87]: Time 8.564353 seconds, bootstrap likelihood -160922.617170, best rearrangement setting 7 Bootstrap[88]: Time 9.266839 seconds, bootstrap likelihood -159413.587872, best rearrangement setting 12 Bootstrap[89]: Time 9.330888 seconds, bootstrap likelihood -159685.190247, best rearrangement setting 10 Bootstrap[90]: Time 8.931364 seconds, bootstrap likelihood -160375.260241, best rearrangement setting 8 Bootstrap[91]: Time 2.975509 seconds, bootstrap likelihood -159745.980633, best rearrangement setting 12 Bootstrap[92]: Time 3.013173 seconds, bootstrap likelihood -161017.018948, best rearrangement setting 13 Bootstrap[93]: Time 9.088764 seconds, bootstrap likelihood -160153.435000, best rearrangement setting 15 Bootstrap[94]: Time 8.015747 seconds, bootstrap likelihood -160771.643696, best rearrangement setting 5 Bootstrap[95]: Time 8.406799 seconds, bootstrap likelihood -158986.472890, best rearrangement setting 5 Bootstrap[96]: Time 8.911972 seconds, bootstrap likelihood -159425.365340, best rearrangement setting 13 Bootstrap[97]: Time 9.405303 seconds, bootstrap likelihood -160826.088457, best rearrangement setting 11 Bootstrap[98]: Time 2.768356 seconds, bootstrap likelihood -160327.805175, best rearrangement setting 6 Bootstrap[99]: Time 9.250451 seconds, bootstrap likelihood -159995.429129, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 998.455727 seconds Average Time per Rapid Bootstrap 9.984557 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 2030.086446 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 100.625985 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.509729 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.313443 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.018789 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 668.883779 seconds Printed linked AA GTR matrix that achieved an overall improvement of 2029.037970 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 100.527712 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.509674 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.313715 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.018785 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1959.543008 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 107.205458 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 7.540695 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.858396 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.137588 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.032975 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -169137.165428 Slow ML Search 1 Likelihood: -169137.160969 Slow ML Search 2 Likelihood: -169137.160967 Slow ML Search 3 Likelihood: -169137.167141 Slow ML Search 4 Likelihood: -169137.160968 Slow ML Search 5 Likelihood: -169137.160968 Slow ML Search 6 Likelihood: -169137.160968 Slow ML Search 7 Likelihood: -169137.160968 Slow ML Search 8 Likelihood: -169137.165219 Slow ML Search 9 Likelihood: -169137.160969 Slow ML optimization finished Slow ML search Time: 1058.011069 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1960.612700 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 107.873330 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 7.627806 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.864774 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.137554 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.032838 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov_Partition_No Name Provided Thorough ML search Time: 691.985991 seconds Final ML Optimization Likelihood: -169134.720983 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.658548 Tree-Length: 19.358964 rate A <-> R: 0.379490 rate A <-> N: 0.474935 rate A <-> D: 2.899885 rate A <-> C: 6.822193 rate A <-> Q: 0.677772 rate A <-> E: 3.006290 rate A <-> G: 7.589900 rate A <-> H: 0.514303 rate A <-> I: 2.006085 rate A <-> L: 1.540113 rate A <-> K: 0.251271 rate A <-> M: 1.774884 rate A <-> F: 0.926281 rate A <-> P: 4.796940 rate A <-> S: 22.790430 rate A <-> T: 15.508659 rate A <-> W: 0.139428 rate A <-> Y: 0.052922 rate A <-> V: 14.298926 rate R <-> N: 0.478446 rate R <-> D: 0.012337 rate R <-> C: 1.277579 rate R <-> Q: 5.864326 rate R <-> E: 1.023419 rate R <-> G: 1.399449 rate R <-> H: 4.526237 rate R <-> I: 0.299579 rate R <-> L: 0.456521 rate R <-> K: 21.186560 rate R <-> M: 1.144139 rate R <-> F: 0.111607 rate R <-> P: 0.546123 rate R <-> S: 1.209831 rate R <-> T: 0.739760 rate R <-> W: 1.158159 rate R <-> Y: 0.428223 rate R <-> V: 0.000000 rate N <-> D: 14.487046 rate N <-> C: 0.869117 rate N <-> Q: 6.857033 rate N <-> E: 3.245182 rate N <-> G: 2.475535 rate N <-> H: 8.252725 rate N <-> I: 2.541746 rate N <-> L: 0.908186 rate N <-> K: 8.382781 rate N <-> M: 0.663734 rate N <-> F: 0.580216 rate N <-> P: 0.434847 rate N <-> S: 14.987140 rate N <-> T: 8.693154 rate N <-> W: 0.205438 rate N <-> Y: 3.628657 rate N <-> V: 0.274657 rate D <-> C: 0.986086 rate D <-> Q: 0.000000 rate D <-> E: 31.797048 rate D <-> G: 2.779715 rate D <-> H: 1.822070 rate D <-> I: 0.113061 rate D <-> L: 0.155462 rate D <-> K: 1.102111 rate D <-> M: 0.000000 rate D <-> F: 0.136379 rate D <-> P: 1.188709 rate D <-> S: 3.488879 rate D <-> T: 1.651293 rate D <-> W: 0.191542 rate D <-> Y: 0.496398 rate D <-> V: 0.489352 rate C <-> Q: 0.184779 rate C <-> E: 0.000000 rate C <-> G: 2.990085 rate C <-> H: 3.232415 rate C <-> I: 1.230282 rate C <-> L: 1.497996 rate C <-> K: 0.000000 rate C <-> M: 2.346945 rate C <-> F: 1.781322 rate C <-> P: 0.000000 rate C <-> S: 9.918830 rate C <-> T: 3.530062 rate C <-> W: 1.517871 rate C <-> Y: 5.083121 rate C <-> V: 4.874410 rate Q <-> E: 7.976748 rate Q <-> G: 0.109258 rate Q <-> H: 23.319837 rate Q <-> I: 0.586945 rate Q <-> L: 1.613063 rate Q <-> K: 7.225298 rate Q <-> M: 1.837507 rate Q <-> F: 0.309242 rate Q <-> P: 4.062817 rate Q <-> S: 2.140410 rate Q <-> T: 2.830524 rate Q <-> W: 0.000000 rate Q <-> Y: 1.542840 rate Q <-> V: 0.161750 rate E <-> G: 3.277358 rate E <-> H: 1.440063 rate E <-> I: 0.302008 rate E <-> L: 0.401022 rate E <-> K: 3.976008 rate E <-> M: 0.098457 rate E <-> F: 0.124894 rate E <-> P: 0.913472 rate E <-> S: 2.340674 rate E <-> T: 1.875981 rate E <-> W: 0.160586 rate E <-> Y: 0.697478 rate E <-> V: 1.082159 rate G <-> H: 0.581689 rate G <-> I: 0.127972 rate G <-> L: 0.039360 rate G <-> K: 0.374931 rate G <-> M: 0.432069 rate G <-> F: 0.262047 rate G <-> P: 0.255438 rate G <-> S: 6.643723 rate G <-> T: 0.657812 rate G <-> W: 1.016867 rate G <-> Y: 0.000000 rate G <-> V: 0.785862 rate H <-> I: 0.211604 rate H <-> L: 0.831229 rate H <-> K: 0.484795 rate H <-> M: 0.000000 rate H <-> F: 0.553086 rate H <-> P: 1.026330 rate H <-> S: 1.792213 rate H <-> T: 1.550901 rate H <-> W: 0.000000 rate H <-> Y: 12.635834 rate H <-> V: 0.000000 rate I <-> L: 17.455022 rate I <-> K: 1.358854 rate I <-> M: 16.101782 rate I <-> F: 3.359910 rate I <-> P: 0.108267 rate I <-> S: 1.076546 rate I <-> T: 8.519227 rate I <-> W: 0.431513 rate I <-> Y: 2.243538 rate I <-> V: 48.625329 rate L <-> K: 0.559658 rate L <-> M: 13.594439 rate L <-> F: 6.105421 rate L <-> P: 1.118512 rate L <-> S: 1.774952 rate L <-> T: 1.782911 rate L <-> W: 1.397125 rate L <-> Y: 1.286310 rate L <-> V: 4.908687 rate K <-> M: 0.490536 rate K <-> F: 0.124924 rate K <-> P: 0.489472 rate K <-> S: 2.024797 rate K <-> T: 1.877385 rate K <-> W: 0.099036 rate K <-> Y: 0.773311 rate K <-> V: 0.266522 rate M <-> F: 1.566770 rate M <-> P: 0.226417 rate M <-> S: 0.611851 rate M <-> T: 5.208694 rate M <-> W: 0.437683 rate M <-> Y: 0.635410 rate M <-> V: 7.716196 rate F <-> P: 0.269994 rate F <-> S: 1.325809 rate F <-> T: 0.682355 rate F <-> W: 1.345946 rate F <-> Y: 10.330774 rate F <-> V: 1.398002 rate P <-> S: 6.326324 rate P <-> T: 3.453808 rate P <-> W: 0.310884 rate P <-> Y: 0.861822 rate P <-> V: 1.488254 rate S <-> T: 22.435128 rate S <-> W: 0.330124 rate S <-> Y: 1.631174 rate S <-> V: 1.559024 rate T <-> W: 0.079287 rate T <-> Y: 0.869866 rate T <-> V: 11.674588 rate W <-> Y: 2.849089 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.043245 freq pi(R): 0.037119 freq pi(N): 0.064533 freq pi(D): 0.028844 freq pi(C): 0.012327 freq pi(Q): 0.017449 freq pi(E): 0.035517 freq pi(G): 0.039518 freq pi(H): 0.016911 freq pi(I): 0.074689 freq pi(L): 0.123516 freq pi(K): 0.080776 freq pi(M): 0.017389 freq pi(F): 0.141912 freq pi(P): 0.021621 freq pi(S): 0.074494 freq pi(T): 0.045034 freq pi(W): 0.015501 freq pi(Y): 0.054199 freq pi(V): 0.055404 ML search took 2418.969718 secs or 0.671936 hours Combined Bootstrap and ML search took 3417.426305 secs or 0.949285 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-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bootstrap.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov Best-scoring ML tree written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov Best-scoring ML tree with support values written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitions.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.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-PROTCATGTR-supermatrix.mito.full-assemblies.80perc_cov Overall execution time for full ML analysis: 3417.492477 secs or 0.949303 hours or 0.039554 days