IMPORTANT WARNING: Alignment column 1 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 3 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 8 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7177 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7178 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7179 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7180 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7181 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7182 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7183 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7184 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7185 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7186 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7187 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7188 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7189 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7190 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7191 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7192 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7193 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7194 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7195 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7196 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7197 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7198 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7945 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7946 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7947 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7948 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7949 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7950 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7951 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7952 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7953 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7954 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7955 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7956 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14225 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14226 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14227 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14228 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14229 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 16924 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 48 columns that contain only undetermined values which will be treated as missing data. Normally these columns should be excluded from the analysis. An alignment file with undetermined columns removed has already been printed to file supermatrix.mito.full-assemblies.fa.reduced 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 12643 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 43.49% 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: 12643 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.fa -n RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 2310.091830 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 163.967423 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 19.444202 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.516061 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_Partition_No Name Provided Time for BS model parameter optimization 485.136354 Bootstrap[0]: Time 545.898727 seconds, bootstrap likelihood -219489.123965, best rearrangement setting 13 Bootstrap[1]: Time 54.702664 seconds, bootstrap likelihood -219109.149550, best rearrangement setting 13 Bootstrap[2]: Time 53.355850 seconds, bootstrap likelihood -215755.878674, best rearrangement setting 12 Bootstrap[3]: Time 56.773469 seconds, bootstrap likelihood -218124.976301, best rearrangement setting 15 Bootstrap[4]: Time 58.736052 seconds, bootstrap likelihood -217921.612887, best rearrangement setting 10 Bootstrap[5]: Time 56.827874 seconds, bootstrap likelihood -218156.281602, best rearrangement setting 10 Bootstrap[6]: Time 53.303559 seconds, bootstrap likelihood -221104.426351, best rearrangement setting 6 Bootstrap[7]: Time 54.990708 seconds, bootstrap likelihood -218695.827448, best rearrangement setting 14 Bootstrap[8]: Time 49.417633 seconds, bootstrap likelihood -220010.127852, best rearrangement setting 5 Bootstrap[9]: Time 54.152172 seconds, bootstrap likelihood -220784.245377, best rearrangement setting 7 Bootstrap[10]: Time 55.219778 seconds, bootstrap likelihood -217327.606201, best rearrangement setting 7 Bootstrap[11]: Time 52.622033 seconds, bootstrap likelihood -219038.776206, best rearrangement setting 5 Bootstrap[12]: Time 57.165294 seconds, bootstrap likelihood -215856.329936, best rearrangement setting 8 Bootstrap[13]: Time 51.407177 seconds, bootstrap likelihood -217925.053941, best rearrangement setting 7 Bootstrap[14]: Time 58.588166 seconds, bootstrap likelihood -216983.911042, best rearrangement setting 12 Bootstrap[15]: Time 55.169060 seconds, bootstrap likelihood -219463.925340, best rearrangement setting 15 Bootstrap[16]: Time 57.409686 seconds, bootstrap likelihood -219960.965560, best rearrangement setting 12 Bootstrap[17]: Time 57.508848 seconds, bootstrap likelihood -217757.090428, best rearrangement setting 12 Bootstrap[18]: Time 52.654294 seconds, bootstrap likelihood -219466.577301, best rearrangement setting 5 Bootstrap[19]: Time 59.271730 seconds, bootstrap likelihood -217324.878522, best rearrangement setting 8 Bootstrap[20]: Time 55.819445 seconds, bootstrap likelihood -221196.237286, best rearrangement setting 10 Bootstrap[21]: Time 55.302798 seconds, bootstrap likelihood -220113.949965, best rearrangement setting 6 Bootstrap[22]: Time 50.210862 seconds, bootstrap likelihood -217989.651516, best rearrangement setting 5 Bootstrap[23]: Time 55.895206 seconds, bootstrap likelihood -214931.389121, best rearrangement setting 7 Bootstrap[24]: Time 58.369785 seconds, bootstrap likelihood -220169.194074, best rearrangement setting 8 Bootstrap[25]: Time 55.230079 seconds, bootstrap likelihood -218694.783519, best rearrangement setting 6 Bootstrap[26]: Time 57.047428 seconds, bootstrap likelihood -219441.721641, best rearrangement setting 12 Bootstrap[27]: Time 56.896188 seconds, bootstrap likelihood -217544.025761, best rearrangement setting 10 Bootstrap[28]: Time 56.624176 seconds, bootstrap likelihood -216853.464857, best rearrangement setting 11 Bootstrap[29]: Time 56.332849 seconds, bootstrap likelihood -217357.042648, best rearrangement setting 12 Bootstrap[30]: Time 18.201480 seconds, bootstrap likelihood -216998.513863, best rearrangement setting 15 Bootstrap[31]: Time 17.582654 seconds, bootstrap likelihood -220099.734497, best rearrangement setting 15 Bootstrap[32]: Time 52.364638 seconds, bootstrap likelihood -217781.132691, best rearrangement setting 6 Bootstrap[33]: Time 53.333467 seconds, bootstrap likelihood -216812.282308, best rearrangement setting 15 Bootstrap[34]: Time 54.321616 seconds, bootstrap likelihood -218005.964460, best rearrangement setting 11 Bootstrap[35]: Time 53.198348 seconds, bootstrap likelihood -218404.944410, best rearrangement setting 8 Bootstrap[36]: Time 53.331964 seconds, bootstrap likelihood -218380.061859, best rearrangement setting 9 Bootstrap[37]: Time 55.086532 seconds, bootstrap likelihood -219501.197324, best rearrangement setting 11 Bootstrap[38]: Time 56.098555 seconds, bootstrap likelihood -220596.471912, best rearrangement setting 8 Bootstrap[39]: Time 17.696043 seconds, bootstrap likelihood -220711.401225, best rearrangement setting 13 Bootstrap[40]: Time 56.977978 seconds, bootstrap likelihood -219054.977383, best rearrangement setting 13 Bootstrap[41]: Time 57.603421 seconds, bootstrap likelihood -217298.520806, best rearrangement setting 10 Bootstrap[42]: Time 49.719150 seconds, bootstrap likelihood -215724.347860, best rearrangement setting 5 Bootstrap[43]: Time 57.642037 seconds, bootstrap likelihood -218099.224182, best rearrangement setting 14 Bootstrap[44]: Time 55.866610 seconds, bootstrap likelihood -218231.819381, best rearrangement setting 10 Bootstrap[45]: Time 57.550379 seconds, bootstrap likelihood -218191.053003, best rearrangement setting 15 Bootstrap[46]: Time 58.657117 seconds, bootstrap likelihood -216950.816082, best rearrangement setting 14 Bootstrap[47]: Time 57.551704 seconds, bootstrap likelihood -219124.189282, best rearrangement setting 8 Bootstrap[48]: Time 54.974321 seconds, bootstrap likelihood -218385.843402, best rearrangement setting 6 Bootstrap[49]: Time 53.072233 seconds, bootstrap likelihood -218758.830287, best rearrangement setting 7 Bootstrap[50]: Time 57.145946 seconds, bootstrap likelihood -219822.537487, best rearrangement setting 7 Bootstrap[51]: Time 54.900970 seconds, bootstrap likelihood -216855.803939, best rearrangement setting 11 Bootstrap[52]: Time 17.942345 seconds, bootstrap likelihood -218324.531041, best rearrangement setting 12 Bootstrap[53]: Time 55.150393 seconds, bootstrap likelihood -219182.400375, best rearrangement setting 8 Bootstrap[54]: Time 55.507828 seconds, bootstrap likelihood -217600.431755, best rearrangement setting 9 Bootstrap[55]: Time 54.592088 seconds, bootstrap likelihood -218408.798014, best rearrangement setting 11 Bootstrap[56]: Time 50.143320 seconds, bootstrap likelihood -218343.337180, best rearrangement setting 5 Bootstrap[57]: Time 51.910595 seconds, bootstrap likelihood -218929.137337, best rearrangement setting 7 Bootstrap[58]: Time 57.602353 seconds, bootstrap likelihood -218011.381050, best rearrangement setting 10 Bootstrap[59]: Time 58.891715 seconds, bootstrap likelihood -217498.420166, best rearrangement setting 9 Bootstrap[60]: Time 57.139772 seconds, bootstrap likelihood -218257.877241, best rearrangement setting 7 Bootstrap[61]: Time 53.368405 seconds, bootstrap likelihood -219138.094848, best rearrangement setting 5 Bootstrap[62]: Time 58.298595 seconds, bootstrap likelihood -218760.480568, best rearrangement setting 11 Bootstrap[63]: Time 58.722676 seconds, bootstrap likelihood -220454.824975, best rearrangement setting 12 Bootstrap[64]: Time 57.444061 seconds, bootstrap likelihood -219110.927281, best rearrangement setting 7 Bootstrap[65]: Time 53.407756 seconds, bootstrap likelihood -220923.688655, best rearrangement setting 5 Bootstrap[66]: Time 50.417049 seconds, bootstrap likelihood -219170.976958, best rearrangement setting 5 Bootstrap[67]: Time 18.444393 seconds, bootstrap likelihood -217428.143538, best rearrangement setting 15 Bootstrap[68]: Time 58.014487 seconds, bootstrap likelihood -218633.531735, best rearrangement setting 11 Bootstrap[69]: Time 52.547908 seconds, bootstrap likelihood -218587.740261, best rearrangement setting 5 Bootstrap[70]: Time 53.600475 seconds, bootstrap likelihood -217766.773243, best rearrangement setting 8 Bootstrap[71]: Time 17.764211 seconds, bootstrap likelihood -217368.938859, best rearrangement setting 10 Bootstrap[72]: Time 57.074536 seconds, bootstrap likelihood -219985.407080, best rearrangement setting 11 Bootstrap[73]: Time 53.952485 seconds, bootstrap likelihood -220125.237841, best rearrangement setting 9 Bootstrap[74]: Time 48.769815 seconds, bootstrap likelihood -218094.698339, best rearrangement setting 5 Bootstrap[75]: Time 55.164230 seconds, bootstrap likelihood -219420.130376, best rearrangement setting 8 Bootstrap[76]: Time 55.296325 seconds, bootstrap likelihood -219351.517173, best rearrangement setting 9 Bootstrap[77]: Time 55.159840 seconds, bootstrap likelihood -220608.690707, best rearrangement setting 11 Bootstrap[78]: Time 55.707676 seconds, bootstrap likelihood -217677.417640, best rearrangement setting 15 Bootstrap[79]: Time 57.202269 seconds, bootstrap likelihood -218400.562745, best rearrangement setting 9 Bootstrap[80]: Time 57.415408 seconds, bootstrap likelihood -217720.403053, best rearrangement setting 15 Bootstrap[81]: Time 55.695394 seconds, bootstrap likelihood -216864.537869, best rearrangement setting 7 Bootstrap[82]: Time 17.954628 seconds, bootstrap likelihood -218296.952531, best rearrangement setting 6 Bootstrap[83]: Time 56.026483 seconds, bootstrap likelihood -220138.827913, best rearrangement setting 10 Bootstrap[84]: Time 54.079765 seconds, bootstrap likelihood -219383.781659, best rearrangement setting 11 Bootstrap[85]: Time 52.994090 seconds, bootstrap likelihood -218676.442369, best rearrangement setting 8 Bootstrap[86]: Time 54.800443 seconds, bootstrap likelihood -217485.768984, best rearrangement setting 7 Bootstrap[87]: Time 54.074216 seconds, bootstrap likelihood -217843.592586, best rearrangement setting 7 Bootstrap[88]: Time 18.681257 seconds, bootstrap likelihood -216983.397615, best rearrangement setting 12 Bootstrap[89]: Time 53.615171 seconds, bootstrap likelihood -219620.706071, best rearrangement setting 10 Bootstrap[90]: Time 54.358225 seconds, bootstrap likelihood -218183.491945, best rearrangement setting 8 Bootstrap[91]: Time 55.479554 seconds, bootstrap likelihood -218630.807991, best rearrangement setting 12 Bootstrap[92]: Time 55.023573 seconds, bootstrap likelihood -219975.687461, best rearrangement setting 13 Bootstrap[93]: Time 57.789305 seconds, bootstrap likelihood -221393.544580, best rearrangement setting 15 Bootstrap[94]: Time 52.232757 seconds, bootstrap likelihood -217904.246295, best rearrangement setting 5 Bootstrap[95]: Time 50.470902 seconds, bootstrap likelihood -218571.376371, best rearrangement setting 5 Bootstrap[96]: Time 55.159090 seconds, bootstrap likelihood -217407.881328, best rearrangement setting 13 Bootstrap[97]: Time 56.369661 seconds, bootstrap likelihood -220972.524404, best rearrangement setting 11 Bootstrap[98]: Time 54.554888 seconds, bootstrap likelihood -217143.578192, best rearrangement setting 6 Bootstrap[99]: Time 54.628551 seconds, bootstrap likelihood -217523.819382, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 5707.005526 seconds Average Time per Rapid Bootstrap 57.070055 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 2311.481844 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 164.794320 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 19.586638 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.541450 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.745920 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.167478 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.046589 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_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 3778.701409 seconds Printed linked AA GTR matrix that achieved an overall improvement of 2309.898796 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 164.674876 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 19.571376 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.530924 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.742102 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.166461 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.046308 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_Partition_No Name Provided Slow ML Search 0 Likelihood: -218573.723863 Slow ML Search 1 Likelihood: -218573.723863 Slow ML Search 2 Likelihood: -218573.723863 Slow ML Search 3 Likelihood: -218573.723863 Slow ML Search 4 Likelihood: -218573.723863 Slow ML Search 5 Likelihood: -218573.723863 Slow ML Search 6 Likelihood: -218573.723863 Slow ML Search 7 Likelihood: -218573.723862 Slow ML Search 8 Likelihood: -218573.723863 Slow ML Search 9 Likelihood: -218573.723862 Slow ML optimization finished Slow ML search Time: 2638.216301 seconds Printed linked AA GTR matrix that achieved an overall improvement of 2310.385232 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 164.054963 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 19.423739 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.507155 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.739670 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.166365 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.046393 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_Partition_No Name Provided Thorough ML search Time: 1072.283495 seconds Final ML Optimization Likelihood: -218573.775425 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.615442 Tree-Length: 26.684955 rate A <-> R: 0.482977 rate A <-> N: 0.621103 rate A <-> D: 2.537416 rate A <-> C: 6.372902 rate A <-> Q: 1.082921 rate A <-> E: 3.770552 rate A <-> G: 7.777592 rate A <-> H: 0.445035 rate A <-> I: 1.819994 rate A <-> L: 1.535812 rate A <-> K: 0.270528 rate A <-> M: 1.558293 rate A <-> F: 0.822188 rate A <-> P: 4.783732 rate A <-> S: 20.933685 rate A <-> T: 15.115938 rate A <-> W: 0.058435 rate A <-> Y: 0.000000 rate A <-> V: 14.576032 rate R <-> N: 0.407153 rate R <-> D: 0.229376 rate R <-> C: 1.799970 rate R <-> Q: 5.672832 rate R <-> E: 0.778038 rate R <-> G: 1.881796 rate R <-> H: 5.368240 rate R <-> I: 0.323368 rate R <-> L: 0.473113 rate R <-> K: 19.775905 rate R <-> M: 1.333920 rate R <-> F: 0.088208 rate R <-> P: 1.164465 rate R <-> S: 1.432476 rate R <-> T: 0.929744 rate R <-> W: 1.445356 rate R <-> Y: 0.467423 rate R <-> V: 0.306072 rate N <-> D: 15.621101 rate N <-> C: 0.960382 rate N <-> Q: 6.617675 rate N <-> E: 2.919506 rate N <-> G: 2.153610 rate N <-> H: 8.345843 rate N <-> I: 2.830885 rate N <-> L: 0.794995 rate N <-> K: 8.294529 rate N <-> M: 0.773395 rate N <-> F: 0.647188 rate N <-> P: 0.356167 rate N <-> S: 14.838141 rate N <-> T: 8.557126 rate N <-> W: 0.115364 rate N <-> Y: 3.383296 rate N <-> V: 0.415197 rate D <-> C: 0.677384 rate D <-> Q: 0.000000 rate D <-> E: 35.459743 rate D <-> G: 3.853821 rate D <-> H: 2.279372 rate D <-> I: 0.296297 rate D <-> L: 0.357603 rate D <-> K: 1.190745 rate D <-> M: 0.051733 rate D <-> F: 0.099046 rate D <-> P: 1.674734 rate D <-> S: 4.199418 rate D <-> T: 2.652134 rate D <-> W: 0.161398 rate D <-> Y: 0.577477 rate D <-> V: 0.751132 rate C <-> Q: 0.129951 rate C <-> E: 0.000000 rate C <-> G: 3.277025 rate C <-> H: 3.628369 rate C <-> I: 1.168681 rate C <-> L: 1.592415 rate C <-> K: 0.000000 rate C <-> M: 1.702992 rate C <-> F: 1.848355 rate C <-> P: 0.029858 rate C <-> S: 9.425937 rate C <-> T: 3.208022 rate C <-> W: 1.290403 rate C <-> Y: 5.353155 rate C <-> V: 4.569479 rate Q <-> E: 8.338919 rate Q <-> G: 0.286373 rate Q <-> H: 24.269086 rate Q <-> I: 0.400439 rate Q <-> L: 1.894493 rate Q <-> K: 7.207143 rate Q <-> M: 1.877161 rate Q <-> F: 0.356993 rate Q <-> P: 4.328218 rate Q <-> S: 2.621493 rate Q <-> T: 2.806691 rate Q <-> W: 0.000000 rate Q <-> Y: 1.968092 rate Q <-> V: 0.581471 rate E <-> G: 3.892996 rate E <-> H: 1.180570 rate E <-> I: 0.395310 rate E <-> L: 0.592740 rate E <-> K: 4.396946 rate E <-> M: 0.237812 rate E <-> F: 0.132863 rate E <-> P: 1.486493 rate E <-> S: 2.771172 rate E <-> T: 3.157467 rate E <-> W: 0.186673 rate E <-> Y: 0.642468 rate E <-> V: 1.127716 rate G <-> H: 0.495208 rate G <-> I: 0.135119 rate G <-> L: 0.070122 rate G <-> K: 0.381097 rate G <-> M: 0.359244 rate G <-> F: 0.221344 rate G <-> P: 0.475159 rate G <-> S: 6.306918 rate G <-> T: 0.492863 rate G <-> W: 1.128404 rate G <-> Y: 0.049829 rate G <-> V: 0.946238 rate H <-> I: 0.201116 rate H <-> L: 1.017983 rate H <-> K: 0.374590 rate H <-> M: 0.000000 rate H <-> F: 0.546493 rate H <-> P: 2.098753 rate H <-> S: 2.096412 rate H <-> T: 1.607130 rate H <-> W: 0.649894 rate H <-> Y: 13.905999 rate H <-> V: 0.000000 rate I <-> L: 16.739122 rate I <-> K: 1.664800 rate I <-> M: 15.192272 rate I <-> F: 3.317483 rate I <-> P: 0.095217 rate I <-> S: 1.142568 rate I <-> T: 8.827728 rate I <-> W: 0.325800 rate I <-> Y: 2.513720 rate I <-> V: 45.829882 rate L <-> K: 0.665034 rate L <-> M: 13.373491 rate L <-> F: 5.805174 rate L <-> P: 1.818778 rate L <-> S: 1.969645 rate L <-> T: 1.931179 rate L <-> W: 1.434993 rate L <-> Y: 1.358547 rate L <-> V: 4.452311 rate K <-> M: 0.650202 rate K <-> F: 0.139309 rate K <-> P: 0.549597 rate K <-> S: 1.905690 rate K <-> T: 1.841356 rate K <-> W: 0.136200 rate K <-> Y: 0.733376 rate K <-> V: 0.344667 rate M <-> F: 1.346636 rate M <-> P: 0.005630 rate M <-> S: 0.561367 rate M <-> T: 5.279860 rate M <-> W: 0.358979 rate M <-> Y: 0.921443 rate M <-> V: 8.862053 rate F <-> P: 0.356246 rate F <-> S: 1.459422 rate F <-> T: 0.697489 rate F <-> W: 1.189791 rate F <-> Y: 9.623885 rate F <-> V: 1.353830 rate P <-> S: 7.240391 rate P <-> T: 3.497268 rate P <-> W: 0.590492 rate P <-> Y: 0.970026 rate P <-> V: 1.888778 rate S <-> T: 21.534070 rate S <-> W: 0.614181 rate S <-> Y: 1.605622 rate S <-> V: 1.530735 rate T <-> W: 0.409758 rate T <-> Y: 1.018805 rate T <-> V: 11.441839 rate W <-> Y: 2.556294 rate W <-> V: 0.159701 rate Y <-> V: 1.000000 freq pi(A): 0.042203 freq pi(R): 0.037092 freq pi(N): 0.066377 freq pi(D): 0.030762 freq pi(C): 0.012280 freq pi(Q): 0.017756 freq pi(E): 0.037922 freq pi(G): 0.039108 freq pi(H): 0.016507 freq pi(I): 0.074642 freq pi(L): 0.123443 freq pi(K): 0.081772 freq pi(M): 0.017046 freq pi(F): 0.138925 freq pi(P): 0.022072 freq pi(S): 0.075230 freq pi(T): 0.044883 freq pi(W): 0.015220 freq pi(Y): 0.053208 freq pi(V): 0.053554 ML search took 7489.294069 secs or 2.080359 hours Combined Bootstrap and ML search took 13196.300467 secs or 3.665639 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 Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bootstrap.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies Best-scoring ML tree written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies 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 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 Overall execution time for full ML analysis: 13196.418903 secs or 3.665672 hours or 0.152736 days