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 7448 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 18.21% 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: 7448 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.95perc_cov.fa -n RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.95perc_cov -m PROTCATGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 10119.090900 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2438.156533 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 135.573243 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.294011 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.95perc_cov_Partition_No Name Provided Time for BS model parameter optimization 122.681961 Bootstrap[0]: Time 125.871942 seconds, bootstrap likelihood -120998.742278, best rearrangement setting 13 Bootstrap[1]: Time 2.410284 seconds, bootstrap likelihood -123634.129078, best rearrangement setting 13 Bootstrap[2]: Time 7.448562 seconds, bootstrap likelihood -122062.884582, best rearrangement setting 12 Bootstrap[3]: Time 7.373252 seconds, bootstrap likelihood -122538.544140, best rearrangement setting 15 Bootstrap[4]: Time 7.434113 seconds, bootstrap likelihood -121345.328806, best rearrangement setting 10 Bootstrap[5]: Time 7.433997 seconds, bootstrap likelihood -121350.993204, best rearrangement setting 10 Bootstrap[6]: Time 7.134327 seconds, bootstrap likelihood -120726.941306, best rearrangement setting 6 Bootstrap[7]: Time 7.109918 seconds, bootstrap likelihood -123276.627030, best rearrangement setting 14 Bootstrap[8]: Time 7.617336 seconds, bootstrap likelihood -122388.326261, best rearrangement setting 5 Bootstrap[9]: Time 2.604015 seconds, bootstrap likelihood -121463.933650, best rearrangement setting 7 Bootstrap[10]: Time 8.075999 seconds, bootstrap likelihood -121944.845382, best rearrangement setting 7 Bootstrap[11]: Time 6.860938 seconds, bootstrap likelihood -122475.804987, best rearrangement setting 5 Bootstrap[12]: Time 7.412563 seconds, bootstrap likelihood -121519.697018, best rearrangement setting 8 Bootstrap[13]: Time 7.609358 seconds, bootstrap likelihood -121385.852304, best rearrangement setting 7 Bootstrap[14]: Time 2.544038 seconds, bootstrap likelihood -122232.616074, best rearrangement setting 12 Bootstrap[15]: Time 8.027533 seconds, bootstrap likelihood -123011.045807, best rearrangement setting 15 Bootstrap[16]: Time 7.406893 seconds, bootstrap likelihood -120867.185061, best rearrangement setting 12 Bootstrap[17]: Time 7.679067 seconds, bootstrap likelihood -121359.386280, best rearrangement setting 12 Bootstrap[18]: Time 6.880028 seconds, bootstrap likelihood -122679.301422, best rearrangement setting 5 Bootstrap[19]: Time 7.507276 seconds, bootstrap likelihood -121862.234595, best rearrangement setting 8 Bootstrap[20]: Time 2.728765 seconds, bootstrap likelihood -121032.781684, best rearrangement setting 10 Bootstrap[21]: Time 7.250149 seconds, bootstrap likelihood -120474.255679, best rearrangement setting 6 Bootstrap[22]: Time 7.138952 seconds, bootstrap likelihood -122618.601890, best rearrangement setting 5 Bootstrap[23]: Time 7.525397 seconds, bootstrap likelihood -121810.398689, best rearrangement setting 7 Bootstrap[24]: Time 7.380951 seconds, bootstrap likelihood -120964.234443, best rearrangement setting 8 Bootstrap[25]: Time 7.282908 seconds, bootstrap likelihood -122337.123838, best rearrangement setting 6 Bootstrap[26]: Time 7.332789 seconds, bootstrap likelihood -121299.228693, best rearrangement setting 12 Bootstrap[27]: Time 7.277111 seconds, bootstrap likelihood -120849.068041, best rearrangement setting 10 Bootstrap[28]: Time 7.214794 seconds, bootstrap likelihood -120754.703712, best rearrangement setting 11 Bootstrap[29]: Time 2.547612 seconds, bootstrap likelihood -122508.208870, best rearrangement setting 12 Bootstrap[30]: Time 8.282081 seconds, bootstrap likelihood -120674.460228, best rearrangement setting 15 Bootstrap[31]: Time 8.181775 seconds, bootstrap likelihood -120388.240727, best rearrangement setting 15 Bootstrap[32]: Time 7.454187 seconds, bootstrap likelihood -122027.249675, best rearrangement setting 6 Bootstrap[33]: Time 7.690527 seconds, bootstrap likelihood -120511.196717, best rearrangement setting 15 Bootstrap[34]: Time 7.328100 seconds, bootstrap likelihood -122629.393635, best rearrangement setting 11 Bootstrap[35]: Time 7.300363 seconds, bootstrap likelihood -122936.666339, best rearrangement setting 8 Bootstrap[36]: Time 2.539758 seconds, bootstrap likelihood -121907.056495, best rearrangement setting 9 Bootstrap[37]: Time 7.702669 seconds, bootstrap likelihood -122735.226355, best rearrangement setting 11 Bootstrap[38]: Time 8.254859 seconds, bootstrap likelihood -123013.326959, best rearrangement setting 8 Bootstrap[39]: Time 2.584991 seconds, bootstrap likelihood -121869.787323, best rearrangement setting 13 Bootstrap[40]: Time 7.309438 seconds, bootstrap likelihood -120542.978951, best rearrangement setting 13 Bootstrap[41]: Time 6.855987 seconds, bootstrap likelihood -122363.578960, best rearrangement setting 10 Bootstrap[42]: Time 6.892379 seconds, bootstrap likelihood -122519.746493, best rearrangement setting 5 Bootstrap[43]: Time 7.571325 seconds, bootstrap likelihood -122413.417896, best rearrangement setting 14 Bootstrap[44]: Time 7.280879 seconds, bootstrap likelihood -121085.117469, best rearrangement setting 10 Bootstrap[45]: Time 2.496331 seconds, bootstrap likelihood -121833.280096, best rearrangement setting 15 Bootstrap[46]: Time 7.532159 seconds, bootstrap likelihood -122196.125958, best rearrangement setting 14 Bootstrap[47]: Time 6.794362 seconds, bootstrap likelihood -121327.545789, best rearrangement setting 8 Bootstrap[48]: Time 2.437960 seconds, bootstrap likelihood -121533.079634, best rearrangement setting 6 Bootstrap[49]: Time 7.730713 seconds, bootstrap likelihood -121113.075461, best rearrangement setting 7 Bootstrap[50]: Time 7.410285 seconds, bootstrap likelihood -122574.165443, best rearrangement setting 7 Bootstrap[51]: Time 7.757393 seconds, bootstrap likelihood -121631.572255, best rearrangement setting 11 Bootstrap[52]: Time 7.753896 seconds, bootstrap likelihood -119907.641084, best rearrangement setting 12 Bootstrap[53]: Time 7.193325 seconds, bootstrap likelihood -120746.001448, best rearrangement setting 8 Bootstrap[54]: Time 7.435971 seconds, bootstrap likelihood -122273.587615, best rearrangement setting 9 Bootstrap[55]: Time 7.543675 seconds, bootstrap likelihood -121287.636814, best rearrangement setting 11 Bootstrap[56]: Time 7.416134 seconds, bootstrap likelihood -121209.643899, best rearrangement setting 5 Bootstrap[57]: Time 7.238673 seconds, bootstrap likelihood -121189.089491, best rearrangement setting 7 Bootstrap[58]: Time 7.475384 seconds, bootstrap likelihood -120193.149765, best rearrangement setting 10 Bootstrap[59]: Time 7.746078 seconds, bootstrap likelihood -123094.003433, best rearrangement setting 9 Bootstrap[60]: Time 2.796646 seconds, bootstrap likelihood -122647.139410, best rearrangement setting 7 Bootstrap[61]: Time 2.549772 seconds, bootstrap likelihood -122524.336348, best rearrangement setting 5 Bootstrap[62]: Time 2.472213 seconds, bootstrap likelihood -122073.445475, best rearrangement setting 11 Bootstrap[63]: Time 2.557128 seconds, bootstrap likelihood -122038.850463, best rearrangement setting 12 Bootstrap[64]: Time 7.318398 seconds, bootstrap likelihood -120837.721710, best rearrangement setting 7 Bootstrap[65]: Time 6.738118 seconds, bootstrap likelihood -122406.010786, best rearrangement setting 5 Bootstrap[66]: Time 6.800215 seconds, bootstrap likelihood -122576.210432, best rearrangement setting 5 Bootstrap[67]: Time 2.525981 seconds, bootstrap likelihood -121554.590499, best rearrangement setting 15 Bootstrap[68]: Time 2.498969 seconds, bootstrap likelihood -121313.403827, best rearrangement setting 11 Bootstrap[69]: Time 6.959173 seconds, bootstrap likelihood -120775.474786, best rearrangement setting 5 Bootstrap[70]: Time 2.902796 seconds, bootstrap likelihood -121965.663141, best rearrangement setting 8 Bootstrap[71]: Time 7.669711 seconds, bootstrap likelihood -122674.537170, best rearrangement setting 10 Bootstrap[72]: Time 7.010976 seconds, bootstrap likelihood -120668.812629, best rearrangement setting 11 Bootstrap[73]: Time 8.036788 seconds, bootstrap likelihood -122202.219558, best rearrangement setting 9 Bootstrap[74]: Time 7.559460 seconds, bootstrap likelihood -121280.416945, best rearrangement setting 5 Bootstrap[75]: Time 2.551768 seconds, bootstrap likelihood -122312.887580, best rearrangement setting 8 Bootstrap[76]: Time 2.528354 seconds, bootstrap likelihood -122583.424127, best rearrangement setting 9 Bootstrap[77]: Time 7.224010 seconds, bootstrap likelihood -121142.694717, best rearrangement setting 11 Bootstrap[78]: Time 7.469172 seconds, bootstrap likelihood -121448.172718, best rearrangement setting 15 Bootstrap[79]: Time 7.463423 seconds, bootstrap likelihood -122011.942443, best rearrangement setting 9 Bootstrap[80]: Time 7.939949 seconds, bootstrap likelihood -122216.867107, best rearrangement setting 15 Bootstrap[81]: Time 7.625937 seconds, bootstrap likelihood -123277.471914, best rearrangement setting 7 Bootstrap[82]: Time 2.486924 seconds, bootstrap likelihood -122315.978556, best rearrangement setting 6 Bootstrap[83]: Time 7.816681 seconds, bootstrap likelihood -122224.972214, best rearrangement setting 10 Bootstrap[84]: Time 8.315724 seconds, bootstrap likelihood -122146.456953, best rearrangement setting 11 Bootstrap[85]: Time 7.815318 seconds, bootstrap likelihood -121322.599683, best rearrangement setting 8 Bootstrap[86]: Time 7.367972 seconds, bootstrap likelihood -122924.368940, best rearrangement setting 7 Bootstrap[87]: Time 7.292271 seconds, bootstrap likelihood -122146.841951, best rearrangement setting 7 Bootstrap[88]: Time 2.514312 seconds, bootstrap likelihood -121078.619000, best rearrangement setting 12 Bootstrap[89]: Time 2.540128 seconds, bootstrap likelihood -122432.785237, best rearrangement setting 10 Bootstrap[90]: Time 7.912379 seconds, bootstrap likelihood -120832.841914, best rearrangement setting 8 Bootstrap[91]: Time 8.055613 seconds, bootstrap likelihood -122839.992542, best rearrangement setting 12 Bootstrap[92]: Time 2.354065 seconds, bootstrap likelihood -122295.866146, best rearrangement setting 13 Bootstrap[93]: Time 7.075300 seconds, bootstrap likelihood -121568.097019, best rearrangement setting 15 Bootstrap[94]: Time 7.278269 seconds, bootstrap likelihood -121244.826525, best rearrangement setting 5 Bootstrap[95]: Time 7.044087 seconds, bootstrap likelihood -121080.644009, best rearrangement setting 5 Bootstrap[96]: Time 8.015760 seconds, bootstrap likelihood -123134.972687, best rearrangement setting 13 Bootstrap[97]: Time 8.237323 seconds, bootstrap likelihood -120514.769268, best rearrangement setting 11 Bootstrap[98]: Time 7.737642 seconds, bootstrap likelihood -122128.376905, best rearrangement setting 6 Bootstrap[99]: Time 7.723745 seconds, bootstrap likelihood -122165.438127, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 758.573397 seconds Average Time per Rapid Bootstrap 7.585734 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 1645.397384 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 77.088478 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.164744 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.189554 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.011695 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.95perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 544.071462 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1645.534036 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 77.100824 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.166491 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.189639 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.011698 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1544.349542 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 77.595608 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.005411 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.487341 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.076242 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.95perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -129024.588232 Slow ML Search 1 Likelihood: -129024.588229 Slow ML Search 2 Likelihood: -129024.588230 Slow ML Search 3 Likelihood: -129024.588230 Slow ML Search 4 Likelihood: -129024.588230 Slow ML Search 5 Likelihood: -129024.588231 Slow ML Search 6 Likelihood: -129024.588231 Slow ML Search 7 Likelihood: -129024.588229 Slow ML Search 8 Likelihood: -129024.588212 Slow ML Search 9 Likelihood: -129024.588232 Slow ML optimization finished Slow ML search Time: 795.166304 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1543.963676 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 77.932133 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.043836 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.486084 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.075346 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.95perc_cov_Partition_No Name Provided Thorough ML search Time: 482.313241 seconds Final ML Optimization Likelihood: -129023.999470 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.682894 Tree-Length: 15.982212 rate A <-> R: 0.367715 rate A <-> N: 0.662112 rate A <-> D: 1.626946 rate A <-> C: 6.047430 rate A <-> Q: 0.256346 rate A <-> E: 2.353702 rate A <-> G: 6.177754 rate A <-> H: 0.288784 rate A <-> I: 2.046813 rate A <-> L: 1.557530 rate A <-> K: 0.178556 rate A <-> M: 1.571588 rate A <-> F: 1.018967 rate A <-> P: 4.206830 rate A <-> S: 23.567016 rate A <-> T: 13.819322 rate A <-> W: 0.000000 rate A <-> Y: 0.047839 rate A <-> V: 13.466973 rate R <-> N: 0.816042 rate R <-> D: 0.000000 rate R <-> C: 1.137610 rate R <-> Q: 5.567879 rate R <-> E: 0.723248 rate R <-> G: 1.031292 rate R <-> H: 3.879274 rate R <-> I: 0.295022 rate R <-> L: 0.369832 rate R <-> K: 22.219393 rate R <-> M: 1.233090 rate R <-> F: 0.163827 rate R <-> P: 0.347777 rate R <-> S: 1.076595 rate R <-> T: 0.652029 rate R <-> W: 0.946520 rate R <-> Y: 0.392062 rate R <-> V: 0.000000 rate N <-> D: 14.933709 rate N <-> C: 0.864752 rate N <-> Q: 7.704625 rate N <-> E: 3.362358 rate N <-> G: 2.705797 rate N <-> H: 9.509338 rate N <-> I: 1.988755 rate N <-> L: 0.866396 rate N <-> K: 8.469533 rate N <-> M: 0.909749 rate N <-> F: 0.427594 rate N <-> P: 0.278535 rate N <-> S: 15.676583 rate N <-> T: 8.859160 rate N <-> W: 0.204610 rate N <-> Y: 3.510025 rate N <-> V: 0.458120 rate D <-> C: 0.918239 rate D <-> Q: 0.000000 rate D <-> E: 30.216768 rate D <-> G: 2.158206 rate D <-> H: 1.966066 rate D <-> I: 0.182527 rate D <-> L: 0.147206 rate D <-> K: 0.998504 rate D <-> M: 0.004428 rate D <-> F: 0.072478 rate D <-> P: 0.459779 rate D <-> S: 3.239637 rate D <-> T: 1.376161 rate D <-> W: 0.252271 rate D <-> Y: 0.527539 rate D <-> V: 0.303616 rate C <-> Q: 0.282336 rate C <-> E: 0.211041 rate C <-> G: 2.673485 rate C <-> H: 2.629130 rate C <-> I: 0.948741 rate C <-> L: 1.586584 rate C <-> K: 0.000000 rate C <-> M: 1.725162 rate C <-> F: 1.902222 rate C <-> P: 0.000000 rate C <-> S: 11.159642 rate C <-> T: 3.871909 rate C <-> W: 1.282030 rate C <-> Y: 3.913732 rate C <-> V: 5.119530 rate Q <-> E: 7.949000 rate Q <-> G: 0.186005 rate Q <-> H: 21.445613 rate Q <-> I: 0.436447 rate Q <-> L: 1.725306 rate Q <-> K: 6.688136 rate Q <-> M: 0.968336 rate Q <-> F: 0.193695 rate Q <-> P: 3.646530 rate Q <-> S: 1.766356 rate Q <-> T: 3.396574 rate Q <-> W: 0.000000 rate Q <-> Y: 1.502771 rate Q <-> V: 0.000000 rate E <-> G: 1.978795 rate E <-> H: 0.353082 rate E <-> I: 0.336091 rate E <-> L: 0.359654 rate E <-> K: 3.791421 rate E <-> M: 0.209006 rate E <-> F: 0.217798 rate E <-> P: 0.211757 rate E <-> S: 2.387031 rate E <-> T: 1.947274 rate E <-> W: 0.168409 rate E <-> Y: 0.986121 rate E <-> V: 0.550679 rate G <-> H: 0.701126 rate G <-> I: 0.126443 rate G <-> L: 0.034710 rate G <-> K: 0.387012 rate G <-> M: 0.395251 rate G <-> F: 0.231663 rate G <-> P: 0.200239 rate G <-> S: 6.178680 rate G <-> T: 0.242341 rate G <-> W: 0.972180 rate G <-> Y: 0.000000 rate G <-> V: 0.580510 rate H <-> I: 0.057542 rate H <-> L: 0.974111 rate H <-> K: 0.273454 rate H <-> M: 0.000000 rate H <-> F: 0.645723 rate H <-> P: 0.484864 rate H <-> S: 1.719806 rate H <-> T: 1.331298 rate H <-> W: 0.000000 rate H <-> Y: 11.403947 rate H <-> V: 0.000000 rate I <-> L: 17.960682 rate I <-> K: 1.152134 rate I <-> M: 15.214285 rate I <-> F: 3.240440 rate I <-> P: 0.144072 rate I <-> S: 0.888849 rate I <-> T: 8.220536 rate I <-> W: 0.427612 rate I <-> Y: 1.649500 rate I <-> V: 51.014716 rate L <-> K: 0.640958 rate L <-> M: 13.751199 rate L <-> F: 6.305312 rate L <-> P: 1.029023 rate L <-> S: 1.765661 rate L <-> T: 1.631931 rate L <-> W: 1.436080 rate L <-> Y: 1.106956 rate L <-> V: 4.585098 rate K <-> M: 0.561433 rate K <-> F: 0.116352 rate K <-> P: 0.396404 rate K <-> S: 2.015617 rate K <-> T: 1.815064 rate K <-> W: 0.115068 rate K <-> Y: 0.674073 rate K <-> V: 0.238280 rate M <-> F: 1.786484 rate M <-> P: 0.338939 rate M <-> S: 0.602468 rate M <-> T: 5.036721 rate M <-> W: 0.417894 rate M <-> Y: 0.208682 rate M <-> V: 7.566854 rate F <-> P: 0.272947 rate F <-> S: 1.310886 rate F <-> T: 0.660285 rate F <-> W: 1.175388 rate F <-> Y: 10.914405 rate F <-> V: 1.303025 rate P <-> S: 5.735780 rate P <-> T: 3.029012 rate P <-> W: 0.364653 rate P <-> Y: 0.635640 rate P <-> V: 0.960197 rate S <-> T: 23.508400 rate S <-> W: 0.335111 rate S <-> Y: 1.560291 rate S <-> V: 1.430847 rate T <-> W: 0.138061 rate T <-> Y: 1.122109 rate T <-> V: 11.400739 rate W <-> Y: 2.943347 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.044035 freq pi(R): 0.038868 freq pi(N): 0.061999 freq pi(D): 0.027489 freq pi(C): 0.013384 freq pi(Q): 0.017010 freq pi(E): 0.032961 freq pi(G): 0.041195 freq pi(H): 0.017824 freq pi(I): 0.076322 freq pi(L): 0.120526 freq pi(K): 0.080988 freq pi(M): 0.018709 freq pi(F): 0.137080 freq pi(P): 0.021790 freq pi(S): 0.074601 freq pi(T): 0.047295 freq pi(W): 0.016403 freq pi(Y): 0.054339 freq pi(V): 0.057183 ML search took 1821.639472 secs or 0.506011 hours Combined Bootstrap and ML search took 2580.213657 secs or 0.716726 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.95perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.95perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.95perc_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.95perc_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.95perc_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.95perc_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.95perc_cov Overall execution time for full ML analysis: 2580.270835 secs or 0.716742 hours or 0.029864 days