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 6329 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 19.29% 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: 6329 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.99perc_cov.fa -n RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.99perc_cov -m PROTCATGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 8531.668432 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2147.077441 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 123.713438 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.892093 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.99perc_cov_Partition_No Name Provided Time for BS model parameter optimization 106.539244 Bootstrap[0]: Time 113.463585 seconds, bootstrap likelihood -102527.360388, best rearrangement setting 13 Bootstrap[1]: Time 6.239288 seconds, bootstrap likelihood -103220.084889, best rearrangement setting 13 Bootstrap[2]: Time 6.611685 seconds, bootstrap likelihood -102531.523221, best rearrangement setting 12 Bootstrap[3]: Time 7.160640 seconds, bootstrap likelihood -102244.937048, best rearrangement setting 15 Bootstrap[4]: Time 2.228660 seconds, bootstrap likelihood -102255.847610, best rearrangement setting 10 Bootstrap[5]: Time 2.353485 seconds, bootstrap likelihood -101807.321315, best rearrangement setting 10 Bootstrap[6]: Time 2.306592 seconds, bootstrap likelihood -102291.204450, best rearrangement setting 6 Bootstrap[7]: Time 7.608632 seconds, bootstrap likelihood -101753.205673, best rearrangement setting 14 Bootstrap[8]: Time 7.025485 seconds, bootstrap likelihood -102438.230452, best rearrangement setting 5 Bootstrap[9]: Time 2.249752 seconds, bootstrap likelihood -103348.532077, best rearrangement setting 7 Bootstrap[10]: Time 6.672744 seconds, bootstrap likelihood -103135.416140, best rearrangement setting 7 Bootstrap[11]: Time 6.990793 seconds, bootstrap likelihood -101186.340687, best rearrangement setting 5 Bootstrap[12]: Time 6.795810 seconds, bootstrap likelihood -101609.973906, best rearrangement setting 8 Bootstrap[13]: Time 2.153220 seconds, bootstrap likelihood -102346.363349, best rearrangement setting 7 Bootstrap[14]: Time 6.481017 seconds, bootstrap likelihood -102027.941444, best rearrangement setting 12 Bootstrap[15]: Time 6.571748 seconds, bootstrap likelihood -101667.185244, best rearrangement setting 15 Bootstrap[16]: Time 2.249431 seconds, bootstrap likelihood -102294.080730, best rearrangement setting 12 Bootstrap[17]: Time 6.256721 seconds, bootstrap likelihood -102732.437575, best rearrangement setting 12 Bootstrap[18]: Time 6.797264 seconds, bootstrap likelihood -102165.168187, best rearrangement setting 5 Bootstrap[19]: Time 6.832784 seconds, bootstrap likelihood -101672.350942, best rearrangement setting 8 Bootstrap[20]: Time 6.464284 seconds, bootstrap likelihood -103533.111001, best rearrangement setting 10 Bootstrap[21]: Time 2.438559 seconds, bootstrap likelihood -102476.698682, best rearrangement setting 6 Bootstrap[22]: Time 6.544542 seconds, bootstrap likelihood -102314.473928, best rearrangement setting 5 Bootstrap[23]: Time 2.232151 seconds, bootstrap likelihood -102539.820425, best rearrangement setting 7 Bootstrap[24]: Time 2.192246 seconds, bootstrap likelihood -100753.458150, best rearrangement setting 8 Bootstrap[25]: Time 6.872620 seconds, bootstrap likelihood -103134.021379, best rearrangement setting 6 Bootstrap[26]: Time 6.921796 seconds, bootstrap likelihood -102447.984909, best rearrangement setting 12 Bootstrap[27]: Time 2.282059 seconds, bootstrap likelihood -101636.268368, best rearrangement setting 10 Bootstrap[28]: Time 2.311796 seconds, bootstrap likelihood -101620.517390, best rearrangement setting 11 Bootstrap[29]: Time 6.681458 seconds, bootstrap likelihood -103143.064957, best rearrangement setting 12 Bootstrap[30]: Time 2.424153 seconds, bootstrap likelihood -100897.857617, best rearrangement setting 15 Bootstrap[31]: Time 6.735947 seconds, bootstrap likelihood -102881.092812, best rearrangement setting 15 Bootstrap[32]: Time 6.881854 seconds, bootstrap likelihood -101601.055539, best rearrangement setting 6 Bootstrap[33]: Time 2.261936 seconds, bootstrap likelihood -101479.392241, best rearrangement setting 15 Bootstrap[34]: Time 2.133274 seconds, bootstrap likelihood -102420.111462, best rearrangement setting 11 Bootstrap[35]: Time 7.287711 seconds, bootstrap likelihood -101899.799208, best rearrangement setting 8 Bootstrap[36]: Time 6.948778 seconds, bootstrap likelihood -101231.768626, best rearrangement setting 9 Bootstrap[37]: Time 6.529517 seconds, bootstrap likelihood -101782.419800, best rearrangement setting 11 Bootstrap[38]: Time 6.910185 seconds, bootstrap likelihood -101938.786194, best rearrangement setting 8 Bootstrap[39]: Time 2.183420 seconds, bootstrap likelihood -101935.027558, best rearrangement setting 13 Bootstrap[40]: Time 2.463591 seconds, bootstrap likelihood -102603.066572, best rearrangement setting 13 Bootstrap[41]: Time 6.445928 seconds, bootstrap likelihood -101487.696533, best rearrangement setting 10 Bootstrap[42]: Time 6.134498 seconds, bootstrap likelihood -101768.144668, best rearrangement setting 5 Bootstrap[43]: Time 6.622847 seconds, bootstrap likelihood -102241.104867, best rearrangement setting 14 Bootstrap[44]: Time 6.539105 seconds, bootstrap likelihood -101942.947548, best rearrangement setting 10 Bootstrap[45]: Time 6.704227 seconds, bootstrap likelihood -102001.727715, best rearrangement setting 15 Bootstrap[46]: Time 6.044640 seconds, bootstrap likelihood -102350.419739, best rearrangement setting 14 Bootstrap[47]: Time 6.661751 seconds, bootstrap likelihood -102133.395252, best rearrangement setting 8 Bootstrap[48]: Time 6.699801 seconds, bootstrap likelihood -103783.391750, best rearrangement setting 6 Bootstrap[49]: Time 2.197893 seconds, bootstrap likelihood -102499.125275, best rearrangement setting 7 Bootstrap[50]: Time 2.428107 seconds, bootstrap likelihood -103414.951098, best rearrangement setting 7 Bootstrap[51]: Time 2.202873 seconds, bootstrap likelihood -102284.933555, best rearrangement setting 11 Bootstrap[52]: Time 6.095815 seconds, bootstrap likelihood -102690.514505, best rearrangement setting 12 Bootstrap[53]: Time 6.834285 seconds, bootstrap likelihood -102298.922602, best rearrangement setting 8 Bootstrap[54]: Time 2.248018 seconds, bootstrap likelihood -102278.589782, best rearrangement setting 9 Bootstrap[55]: Time 2.244707 seconds, bootstrap likelihood -102477.524679, best rearrangement setting 11 Bootstrap[56]: Time 6.186389 seconds, bootstrap likelihood -102263.267848, best rearrangement setting 5 Bootstrap[57]: Time 6.425025 seconds, bootstrap likelihood -103206.000416, best rearrangement setting 7 Bootstrap[58]: Time 6.795142 seconds, bootstrap likelihood -102312.282299, best rearrangement setting 10 Bootstrap[59]: Time 6.860557 seconds, bootstrap likelihood -102463.991921, best rearrangement setting 9 Bootstrap[60]: Time 2.375028 seconds, bootstrap likelihood -101158.657316, best rearrangement setting 7 Bootstrap[61]: Time 2.171179 seconds, bootstrap likelihood -101935.658710, best rearrangement setting 5 Bootstrap[62]: Time 6.920736 seconds, bootstrap likelihood -102755.813999, best rearrangement setting 11 Bootstrap[63]: Time 6.876048 seconds, bootstrap likelihood -102262.804687, best rearrangement setting 12 Bootstrap[64]: Time 2.218836 seconds, bootstrap likelihood -101891.711495, best rearrangement setting 7 Bootstrap[65]: Time 2.191959 seconds, bootstrap likelihood -100688.577572, best rearrangement setting 5 Bootstrap[66]: Time 2.209684 seconds, bootstrap likelihood -100930.835700, best rearrangement setting 5 Bootstrap[67]: Time 2.187813 seconds, bootstrap likelihood -101418.125762, best rearrangement setting 15 Bootstrap[68]: Time 7.012008 seconds, bootstrap likelihood -103199.531616, best rearrangement setting 11 Bootstrap[69]: Time 6.175424 seconds, bootstrap likelihood -101555.668630, best rearrangement setting 5 Bootstrap[70]: Time 2.509015 seconds, bootstrap likelihood -103592.244913, best rearrangement setting 8 Bootstrap[71]: Time 2.319679 seconds, bootstrap likelihood -101991.501446, best rearrangement setting 10 Bootstrap[72]: Time 2.186228 seconds, bootstrap likelihood -101812.349994, best rearrangement setting 11 Bootstrap[73]: Time 2.187701 seconds, bootstrap likelihood -102029.313619, best rearrangement setting 9 Bootstrap[74]: Time 2.305940 seconds, bootstrap likelihood -102663.587345, best rearrangement setting 5 Bootstrap[75]: Time 2.232149 seconds, bootstrap likelihood -102506.391607, best rearrangement setting 8 Bootstrap[76]: Time 6.828827 seconds, bootstrap likelihood -102909.195336, best rearrangement setting 9 Bootstrap[77]: Time 6.817659 seconds, bootstrap likelihood -101955.611890, best rearrangement setting 11 Bootstrap[78]: Time 6.627525 seconds, bootstrap likelihood -102158.608533, best rearrangement setting 15 Bootstrap[79]: Time 2.308570 seconds, bootstrap likelihood -102163.492966, best rearrangement setting 9 Bootstrap[80]: Time 2.412440 seconds, bootstrap likelihood -102505.434377, best rearrangement setting 15 Bootstrap[81]: Time 2.163125 seconds, bootstrap likelihood -102025.863571, best rearrangement setting 7 Bootstrap[82]: Time 2.265334 seconds, bootstrap likelihood -104211.361846, best rearrangement setting 6 Bootstrap[83]: Time 2.312966 seconds, bootstrap likelihood -101232.010937, best rearrangement setting 10 Bootstrap[84]: Time 6.623501 seconds, bootstrap likelihood -102298.669707, best rearrangement setting 11 Bootstrap[85]: Time 6.629511 seconds, bootstrap likelihood -102154.802824, best rearrangement setting 8 Bootstrap[86]: Time 6.964576 seconds, bootstrap likelihood -102451.858941, best rearrangement setting 7 Bootstrap[87]: Time 6.449716 seconds, bootstrap likelihood -101586.731238, best rearrangement setting 7 Bootstrap[88]: Time 6.717415 seconds, bootstrap likelihood -103111.105779, best rearrangement setting 12 Bootstrap[89]: Time 6.948958 seconds, bootstrap likelihood -103665.904131, best rearrangement setting 10 Bootstrap[90]: Time 6.724700 seconds, bootstrap likelihood -102258.140420, best rearrangement setting 8 Bootstrap[91]: Time 6.134935 seconds, bootstrap likelihood -101681.816619, best rearrangement setting 12 Bootstrap[92]: Time 2.286199 seconds, bootstrap likelihood -102178.531844, best rearrangement setting 13 Bootstrap[93]: Time 2.185889 seconds, bootstrap likelihood -101900.980845, best rearrangement setting 15 Bootstrap[94]: Time 2.151680 seconds, bootstrap likelihood -102284.068479, best rearrangement setting 5 Bootstrap[95]: Time 6.081466 seconds, bootstrap likelihood -102242.406489, best rearrangement setting 5 Bootstrap[96]: Time 6.757113 seconds, bootstrap likelihood -101384.188495, best rearrangement setting 13 Bootstrap[97]: Time 6.905142 seconds, bootstrap likelihood -101563.608099, best rearrangement setting 11 Bootstrap[98]: Time 6.610644 seconds, bootstrap likelihood -102103.363511, best rearrangement setting 6 Bootstrap[99]: Time 6.497264 seconds, bootstrap likelihood -103160.952968, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 593.895529 seconds Average Time per Rapid Bootstrap 5.938955 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 1400.659373 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 69.571783 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.870872 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.156345 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.010251 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.99perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 488.681183 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1398.259554 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 69.468078 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.867372 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.155870 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.010245 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1319.887673 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 71.074195 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.901130 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.498033 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.077223 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.99perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -108450.009010 Slow ML Search 1 Likelihood: -108450.009010 Slow ML Search 2 Likelihood: -108450.009010 Slow ML Search 3 Likelihood: -108450.009014 Slow ML Search 4 Likelihood: -108450.009013 Slow ML Search 5 Likelihood: -108450.009014 Slow ML Search 6 Likelihood: -108450.009011 Slow ML Search 7 Likelihood: -108450.009014 Slow ML Search 8 Likelihood: -108450.009014 Slow ML Search 9 Likelihood: -108450.009014 Slow ML optimization finished Slow ML search Time: 686.325419 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1324.568047 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 71.691650 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.013081 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.505590 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.99perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.077070 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.99perc_cov_Partition_No Name Provided Thorough ML search Time: 414.893666 seconds Final ML Optimization Likelihood: -108447.467385 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.665662 Tree-Length: 16.151323 rate A <-> R: 0.480462 rate A <-> N: 0.606575 rate A <-> D: 1.696780 rate A <-> C: 5.835517 rate A <-> Q: 0.219655 rate A <-> E: 2.502282 rate A <-> G: 6.616814 rate A <-> H: 0.000000 rate A <-> I: 2.118554 rate A <-> L: 1.627844 rate A <-> K: 0.081462 rate A <-> M: 1.879725 rate A <-> F: 1.067006 rate A <-> P: 4.430277 rate A <-> S: 23.455454 rate A <-> T: 14.775468 rate A <-> W: 0.000000 rate A <-> Y: 0.008800 rate A <-> V: 13.282307 rate R <-> N: 0.761492 rate R <-> D: 0.000000 rate R <-> C: 0.960368 rate R <-> Q: 5.384885 rate R <-> E: 0.684963 rate R <-> G: 0.990301 rate R <-> H: 3.900653 rate R <-> I: 0.181426 rate R <-> L: 0.393947 rate R <-> K: 21.432744 rate R <-> M: 1.280186 rate R <-> F: 0.107946 rate R <-> P: 0.276400 rate R <-> S: 1.088149 rate R <-> T: 0.546157 rate R <-> W: 1.028094 rate R <-> Y: 0.413680 rate R <-> V: 0.000000 rate N <-> D: 15.099004 rate N <-> C: 0.484330 rate N <-> Q: 7.418873 rate N <-> E: 3.151006 rate N <-> G: 2.697917 rate N <-> H: 9.415380 rate N <-> I: 2.089841 rate N <-> L: 0.971733 rate N <-> K: 8.452523 rate N <-> M: 0.772445 rate N <-> F: 0.470494 rate N <-> P: 0.000000 rate N <-> S: 16.061031 rate N <-> T: 8.440058 rate N <-> W: 0.140758 rate N <-> Y: 3.634361 rate N <-> V: 0.430383 rate D <-> C: 1.102094 rate D <-> Q: 0.000000 rate D <-> E: 30.229629 rate D <-> G: 1.708224 rate D <-> H: 2.244348 rate D <-> I: 0.231307 rate D <-> L: 0.111328 rate D <-> K: 1.064418 rate D <-> M: 0.000000 rate D <-> F: 0.000000 rate D <-> P: 0.546446 rate D <-> S: 3.173182 rate D <-> T: 1.172582 rate D <-> W: 0.333413 rate D <-> Y: 0.691352 rate D <-> V: 0.083547 rate C <-> Q: 0.366156 rate C <-> E: 0.211537 rate C <-> G: 2.030089 rate C <-> H: 2.821849 rate C <-> I: 0.730533 rate C <-> L: 0.983222 rate C <-> K: 0.000000 rate C <-> M: 2.557991 rate C <-> F: 1.820405 rate C <-> P: 0.000000 rate C <-> S: 10.911923 rate C <-> T: 4.358140 rate C <-> W: 1.213766 rate C <-> Y: 3.644492 rate C <-> V: 5.612662 rate Q <-> E: 8.668351 rate Q <-> G: 0.000000 rate Q <-> H: 20.432818 rate Q <-> I: 0.513267 rate Q <-> L: 2.023915 rate Q <-> K: 6.669541 rate Q <-> M: 0.981777 rate Q <-> F: 0.050255 rate Q <-> P: 3.325769 rate Q <-> S: 1.311495 rate Q <-> T: 3.620657 rate Q <-> W: 0.000000 rate Q <-> Y: 1.996372 rate Q <-> V: 0.000000 rate E <-> G: 2.015684 rate E <-> H: 0.349195 rate E <-> I: 0.351537 rate E <-> L: 0.384547 rate E <-> K: 3.701356 rate E <-> M: 0.309184 rate E <-> F: 0.223463 rate E <-> P: 0.237484 rate E <-> S: 2.329701 rate E <-> T: 2.165653 rate E <-> W: 0.208490 rate E <-> Y: 1.115392 rate E <-> V: 0.413226 rate G <-> H: 0.690139 rate G <-> I: 0.157217 rate G <-> L: 0.037212 rate G <-> K: 0.453973 rate G <-> M: 0.440823 rate G <-> F: 0.274392 rate G <-> P: 0.000000 rate G <-> S: 6.237653 rate G <-> T: 0.323647 rate G <-> W: 0.951244 rate G <-> Y: 0.000000 rate G <-> V: 0.568707 rate H <-> I: 0.042238 rate H <-> L: 0.859478 rate H <-> K: 0.223681 rate H <-> M: 0.000000 rate H <-> F: 0.555900 rate H <-> P: 0.679481 rate H <-> S: 1.842860 rate H <-> T: 0.889643 rate H <-> W: 0.067030 rate H <-> Y: 10.497406 rate H <-> V: 0.000000 rate I <-> L: 17.810053 rate I <-> K: 1.205479 rate I <-> M: 15.659292 rate I <-> F: 3.434726 rate I <-> P: 0.234035 rate I <-> S: 0.724691 rate I <-> T: 8.324970 rate I <-> W: 0.349722 rate I <-> Y: 1.397554 rate I <-> V: 50.538004 rate L <-> K: 0.602611 rate L <-> M: 14.142110 rate L <-> F: 6.347965 rate L <-> P: 0.696466 rate L <-> S: 1.728908 rate L <-> T: 1.678594 rate L <-> W: 1.373648 rate L <-> Y: 1.112007 rate L <-> V: 4.478800 rate K <-> M: 0.626826 rate K <-> F: 0.086602 rate K <-> P: 0.337482 rate K <-> S: 1.829523 rate K <-> T: 2.122744 rate K <-> W: 0.091878 rate K <-> Y: 0.654643 rate K <-> V: 0.302382 rate M <-> F: 1.703149 rate M <-> P: 0.400801 rate M <-> S: 0.819224 rate M <-> T: 5.471028 rate M <-> W: 0.000000 rate M <-> Y: 0.188274 rate M <-> V: 7.072718 rate F <-> P: 0.262996 rate F <-> S: 1.369085 rate F <-> T: 0.674248 rate F <-> W: 1.280114 rate F <-> Y: 11.512492 rate F <-> V: 1.324032 rate P <-> S: 5.746228 rate P <-> T: 1.986555 rate P <-> W: 0.000000 rate P <-> Y: 0.603094 rate P <-> V: 0.972423 rate S <-> T: 24.256302 rate S <-> W: 0.429436 rate S <-> Y: 1.631369 rate S <-> V: 1.234508 rate T <-> W: 0.123278 rate T <-> Y: 1.334051 rate T <-> V: 11.413700 rate W <-> Y: 2.343870 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.043449 freq pi(R): 0.041227 freq pi(N): 0.061654 freq pi(D): 0.027734 freq pi(C): 0.013765 freq pi(Q): 0.017171 freq pi(E): 0.033568 freq pi(G): 0.042152 freq pi(H): 0.018510 freq pi(I): 0.076523 freq pi(L): 0.120533 freq pi(K): 0.081282 freq pi(M): 0.018690 freq pi(F): 0.132862 freq pi(P): 0.022913 freq pi(S): 0.073372 freq pi(T): 0.046676 freq pi(W): 0.015991 freq pi(Y): 0.054569 freq pi(V): 0.057360 ML search took 1589.987753 secs or 0.441663 hours Combined Bootstrap and ML search took 2183.884093 secs or 0.606634 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.99perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.99perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.99perc_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.99perc_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.99perc_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.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-PROTCATGTR-supermatrix.mito.full-assemblies.99perc_cov Overall execution time for full ML analysis: 2184.081186 secs or 0.606689 hours or 0.025279 days