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 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: 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-PROTGAMMAGTR-supermatrix.mito.full-assemblies.95perc_cov -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 1543.967065 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 77.465982 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.989076 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.95perc_cov_Partition_No Name Provided Time for BS model parameter optimization 225.003038 Bootstrap[0]: Time 255.985620 seconds, bootstrap likelihood -128087.398786, best rearrangement setting 13 Bootstrap[1]: Time 29.293738 seconds, bootstrap likelihood -130980.622561, best rearrangement setting 13 Bootstrap[2]: Time 27.633361 seconds, bootstrap likelihood -129114.904192, best rearrangement setting 12 Bootstrap[3]: Time 8.917869 seconds, bootstrap likelihood -129754.633101, best rearrangement setting 15 Bootstrap[4]: Time 9.052660 seconds, bootstrap likelihood -128499.013312, best rearrangement setting 10 Bootstrap[5]: Time 9.274737 seconds, bootstrap likelihood -128469.176273, best rearrangement setting 10 Bootstrap[6]: Time 8.444688 seconds, bootstrap likelihood -127867.212719, best rearrangement setting 6 Bootstrap[7]: Time 8.175008 seconds, bootstrap likelihood -130447.115402, best rearrangement setting 14 Bootstrap[8]: Time 9.450074 seconds, bootstrap likelihood -129714.508073, best rearrangement setting 5 Bootstrap[9]: Time 29.924003 seconds, bootstrap likelihood -128608.129615, best rearrangement setting 7 Bootstrap[10]: Time 29.034672 seconds, bootstrap likelihood -129188.748870, best rearrangement setting 7 Bootstrap[11]: Time 24.391892 seconds, bootstrap likelihood -129647.008790, best rearrangement setting 5 Bootstrap[12]: Time 29.134314 seconds, bootstrap likelihood -128657.625839, best rearrangement setting 8 Bootstrap[13]: Time 28.138049 seconds, bootstrap likelihood -128414.104151, best rearrangement setting 7 Bootstrap[14]: Time 28.842747 seconds, bootstrap likelihood -129380.868522, best rearrangement setting 12 Bootstrap[15]: Time 28.670273 seconds, bootstrap likelihood -130276.996100, best rearrangement setting 15 Bootstrap[16]: Time 8.949077 seconds, bootstrap likelihood -128060.249198, best rearrangement setting 12 Bootstrap[17]: Time 29.503250 seconds, bootstrap likelihood -128473.552900, best rearrangement setting 12 Bootstrap[18]: Time 25.917792 seconds, bootstrap likelihood -129818.166443, best rearrangement setting 5 Bootstrap[19]: Time 26.541227 seconds, bootstrap likelihood -129036.267648, best rearrangement setting 8 Bootstrap[20]: Time 28.983431 seconds, bootstrap likelihood -128183.977266, best rearrangement setting 10 Bootstrap[21]: Time 28.145478 seconds, bootstrap likelihood -127524.143106, best rearrangement setting 6 Bootstrap[22]: Time 25.336047 seconds, bootstrap likelihood -129793.158794, best rearrangement setting 5 Bootstrap[23]: Time 27.393704 seconds, bootstrap likelihood -129048.302990, best rearrangement setting 7 Bootstrap[24]: Time 8.378766 seconds, bootstrap likelihood -128186.995500, best rearrangement setting 8 Bootstrap[25]: Time 28.454663 seconds, bootstrap likelihood -129542.212951, best rearrangement setting 6 Bootstrap[26]: Time 27.266802 seconds, bootstrap likelihood -128376.438322, best rearrangement setting 12 Bootstrap[27]: Time 28.671895 seconds, bootstrap likelihood -127924.581214, best rearrangement setting 10 Bootstrap[28]: Time 28.852547 seconds, bootstrap likelihood -127887.014874, best rearrangement setting 11 Bootstrap[29]: Time 30.324406 seconds, bootstrap likelihood -129799.950261, best rearrangement setting 12 Bootstrap[30]: Time 29.785655 seconds, bootstrap likelihood -127724.031640, best rearrangement setting 15 Bootstrap[31]: Time 29.377118 seconds, bootstrap likelihood -127459.791987, best rearrangement setting 15 Bootstrap[32]: Time 29.469842 seconds, bootstrap likelihood -129151.693131, best rearrangement setting 6 Bootstrap[33]: Time 29.747203 seconds, bootstrap likelihood -127653.192465, best rearrangement setting 15 Bootstrap[34]: Time 29.556052 seconds, bootstrap likelihood -129739.191508, best rearrangement setting 11 Bootstrap[35]: Time 29.731936 seconds, bootstrap likelihood -130102.712685, best rearrangement setting 8 Bootstrap[36]: Time 9.418747 seconds, bootstrap likelihood -129069.066313, best rearrangement setting 9 Bootstrap[37]: Time 29.751797 seconds, bootstrap likelihood -130000.144817, best rearrangement setting 11 Bootstrap[38]: Time 28.612131 seconds, bootstrap likelihood -130300.622423, best rearrangement setting 8 Bootstrap[39]: Time 29.740869 seconds, bootstrap likelihood -129053.707850, best rearrangement setting 13 Bootstrap[40]: Time 28.524068 seconds, bootstrap likelihood -127578.217064, best rearrangement setting 13 Bootstrap[41]: Time 28.351683 seconds, bootstrap likelihood -129577.322856, best rearrangement setting 10 Bootstrap[42]: Time 26.877057 seconds, bootstrap likelihood -129717.823205, best rearrangement setting 5 Bootstrap[43]: Time 28.664745 seconds, bootstrap likelihood -129576.052022, best rearrangement setting 14 Bootstrap[44]: Time 29.315638 seconds, bootstrap likelihood -128125.665711, best rearrangement setting 10 Bootstrap[45]: Time 30.222781 seconds, bootstrap likelihood -129081.264784, best rearrangement setting 15 Bootstrap[46]: Time 30.019756 seconds, bootstrap likelihood -129392.159680, best rearrangement setting 14 Bootstrap[47]: Time 26.359933 seconds, bootstrap likelihood -128451.923174, best rearrangement setting 8 Bootstrap[48]: Time 9.177331 seconds, bootstrap likelihood -128622.699804, best rearrangement setting 6 Bootstrap[49]: Time 28.047235 seconds, bootstrap likelihood -128302.836950, best rearrangement setting 7 Bootstrap[50]: Time 27.373841 seconds, bootstrap likelihood -129822.155294, best rearrangement setting 7 Bootstrap[51]: Time 27.217579 seconds, bootstrap likelihood -128636.050494, best rearrangement setting 11 Bootstrap[52]: Time 28.075673 seconds, bootstrap likelihood -127027.940222, best rearrangement setting 12 Bootstrap[53]: Time 28.135996 seconds, bootstrap likelihood -127823.032280, best rearrangement setting 8 Bootstrap[54]: Time 29.599128 seconds, bootstrap likelihood -129490.692561, best rearrangement setting 9 Bootstrap[55]: Time 26.841118 seconds, bootstrap likelihood -128368.394763, best rearrangement setting 11 Bootstrap[56]: Time 25.737268 seconds, bootstrap likelihood -128279.952021, best rearrangement setting 5 Bootstrap[57]: Time 8.656953 seconds, bootstrap likelihood -128352.040126, best rearrangement setting 7 Bootstrap[58]: Time 27.565106 seconds, bootstrap likelihood -127300.738714, best rearrangement setting 10 Bootstrap[59]: Time 28.535926 seconds, bootstrap likelihood -130336.424723, best rearrangement setting 9 Bootstrap[60]: Time 9.584781 seconds, bootstrap likelihood -129875.292819, best rearrangement setting 7 Bootstrap[61]: Time 26.204621 seconds, bootstrap likelihood -129635.500027, best rearrangement setting 5 Bootstrap[62]: Time 28.404344 seconds, bootstrap likelihood -129249.331043, best rearrangement setting 11 Bootstrap[63]: Time 9.280203 seconds, bootstrap likelihood -129273.173830, best rearrangement setting 12 Bootstrap[64]: Time 26.271639 seconds, bootstrap likelihood -127875.372704, best rearrangement setting 7 Bootstrap[65]: Time 24.476885 seconds, bootstrap likelihood -129605.597484, best rearrangement setting 5 Bootstrap[66]: Time 26.891468 seconds, bootstrap likelihood -129829.038595, best rearrangement setting 5 Bootstrap[67]: Time 29.025517 seconds, bootstrap likelihood -128804.854728, best rearrangement setting 15 Bootstrap[68]: Time 29.207454 seconds, bootstrap likelihood -128407.552023, best rearrangement setting 11 Bootstrap[69]: Time 27.248158 seconds, bootstrap likelihood -127946.233461, best rearrangement setting 5 Bootstrap[70]: Time 28.968554 seconds, bootstrap likelihood -129124.900416, best rearrangement setting 8 Bootstrap[71]: Time 29.988259 seconds, bootstrap likelihood -129884.641743, best rearrangement setting 10 Bootstrap[72]: Time 26.979827 seconds, bootstrap likelihood -127748.164502, best rearrangement setting 11 Bootstrap[73]: Time 27.731930 seconds, bootstrap likelihood -129341.214325, best rearrangement setting 9 Bootstrap[74]: Time 27.259873 seconds, bootstrap likelihood -128430.983944, best rearrangement setting 5 Bootstrap[75]: Time 29.304984 seconds, bootstrap likelihood -129532.056633, best rearrangement setting 8 Bootstrap[76]: Time 27.394956 seconds, bootstrap likelihood -129675.169545, best rearrangement setting 9 Bootstrap[77]: Time 29.886275 seconds, bootstrap likelihood -128242.922823, best rearrangement setting 11 Bootstrap[78]: Time 28.239385 seconds, bootstrap likelihood -128605.513912, best rearrangement setting 15 Bootstrap[79]: Time 27.987247 seconds, bootstrap likelihood -129145.659937, best rearrangement setting 9 Bootstrap[80]: Time 28.097705 seconds, bootstrap likelihood -129398.820736, best rearrangement setting 15 Bootstrap[81]: Time 29.816443 seconds, bootstrap likelihood -130498.072800, best rearrangement setting 7 Bootstrap[82]: Time 8.744088 seconds, bootstrap likelihood -129523.587402, best rearrangement setting 6 Bootstrap[83]: Time 26.248774 seconds, bootstrap likelihood -129448.901765, best rearrangement setting 10 Bootstrap[84]: Time 28.836450 seconds, bootstrap likelihood -129256.871721, best rearrangement setting 11 Bootstrap[85]: Time 28.602863 seconds, bootstrap likelihood -128419.255178, best rearrangement setting 8 Bootstrap[86]: Time 28.597012 seconds, bootstrap likelihood -130055.112597, best rearrangement setting 7 Bootstrap[87]: Time 29.055275 seconds, bootstrap likelihood -129360.645869, best rearrangement setting 7 Bootstrap[88]: Time 8.806126 seconds, bootstrap likelihood -128224.787049, best rearrangement setting 12 Bootstrap[89]: Time 8.796246 seconds, bootstrap likelihood -129578.798960, best rearrangement setting 10 Bootstrap[90]: Time 30.637343 seconds, bootstrap likelihood -127958.803972, best rearrangement setting 8 Bootstrap[91]: Time 27.675788 seconds, bootstrap likelihood -129963.341239, best rearrangement setting 12 Bootstrap[92]: Time 27.409408 seconds, bootstrap likelihood -129448.122591, best rearrangement setting 13 Bootstrap[93]: Time 8.366218 seconds, bootstrap likelihood -128700.047274, best rearrangement setting 15 Bootstrap[94]: Time 25.445801 seconds, bootstrap likelihood -128386.570770, best rearrangement setting 5 Bootstrap[95]: Time 25.252157 seconds, bootstrap likelihood -128207.431830, best rearrangement setting 5 Bootstrap[96]: Time 26.628282 seconds, bootstrap likelihood -130376.730667, best rearrangement setting 13 Bootstrap[97]: Time 29.876820 seconds, bootstrap likelihood -127532.081569, best rearrangement setting 11 Bootstrap[98]: Time 9.407614 seconds, bootstrap likelihood -129298.698597, best rearrangement setting 6 Bootstrap[99]: Time 29.462870 seconds, bootstrap likelihood -129321.985800, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 2702.062131 seconds Average Time per Rapid Bootstrap 27.020621 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 1551.126984 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 76.656224 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.988655 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.487020 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.074623 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.95perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 2074.682229 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1543.969779 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 77.545962 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.000588 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.486882 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.076181 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.95perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -129024.019673 Slow ML Search 1 Likelihood: -129024.019671 Slow ML Search 2 Likelihood: -129024.019671 Slow ML Search 3 Likelihood: -129024.019671 Slow ML Search 4 Likelihood: -129024.019671 Slow ML Search 5 Likelihood: -129024.019671 Slow ML Search 6 Likelihood: -129024.019671 Slow ML Search 7 Likelihood: -129024.019671 Slow ML Search 8 Likelihood: -129024.019671 Slow ML Search 9 Likelihood: -129024.019673 Slow ML optimization finished Slow ML search Time: 1289.944478 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1544.035000 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 77.496130 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.010105 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.490689 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.95perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.077263 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.95perc_cov_Partition_No Name Provided Thorough ML search Time: 486.257664 seconds Final ML Optimization Likelihood: -129024.019868 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.682949 Tree-Length: 15.980403 rate A <-> R: 0.366888 rate A <-> N: 0.660574 rate A <-> D: 1.623283 rate A <-> C: 6.033785 rate A <-> Q: 0.255666 rate A <-> E: 2.348335 rate A <-> G: 6.163352 rate A <-> H: 0.288216 rate A <-> I: 2.042368 rate A <-> L: 1.553892 rate A <-> K: 0.178146 rate A <-> M: 1.568211 rate A <-> F: 1.016620 rate A <-> P: 4.197054 rate A <-> S: 23.512394 rate A <-> T: 13.787255 rate A <-> W: 0.000000 rate A <-> Y: 0.047631 rate A <-> V: 13.435119 rate R <-> N: 0.814106 rate R <-> D: 0.000000 rate R <-> C: 1.134950 rate R <-> Q: 5.554974 rate R <-> E: 0.721590 rate R <-> G: 1.028967 rate R <-> H: 3.870556 rate R <-> I: 0.294374 rate R <-> L: 0.368973 rate R <-> K: 22.167874 rate R <-> M: 1.230346 rate R <-> F: 0.163416 rate R <-> P: 0.346947 rate R <-> S: 1.074194 rate R <-> T: 0.650608 rate R <-> W: 0.944307 rate R <-> Y: 0.391362 rate R <-> V: 0.000000 rate N <-> D: 14.899504 rate N <-> C: 0.862799 rate N <-> Q: 7.686781 rate N <-> E: 3.354606 rate N <-> G: 2.699661 rate N <-> H: 9.487424 rate N <-> I: 1.984139 rate N <-> L: 0.864405 rate N <-> K: 8.450256 rate N <-> M: 0.907650 rate N <-> F: 0.426640 rate N <-> P: 0.277952 rate N <-> S: 15.640405 rate N <-> T: 8.838801 rate N <-> W: 0.204104 rate N <-> Y: 3.502001 rate N <-> V: 0.457151 rate D <-> C: 0.916038 rate D <-> Q: 0.000000 rate D <-> E: 30.147003 rate D <-> G: 2.153263 rate D <-> H: 1.961836 rate D <-> I: 0.182120 rate D <-> L: 0.146879 rate D <-> K: 0.996296 rate D <-> M: 0.004388 rate D <-> F: 0.072324 rate D <-> P: 0.458645 rate D <-> S: 3.232386 rate D <-> T: 1.373054 rate D <-> W: 0.251708 rate D <-> Y: 0.526374 rate D <-> V: 0.302858 rate C <-> Q: 0.281652 rate C <-> E: 0.210659 rate C <-> G: 2.667302 rate C <-> H: 2.622276 rate C <-> I: 0.946578 rate C <-> L: 1.583167 rate C <-> K: 0.000000 rate C <-> M: 1.721213 rate C <-> F: 1.897985 rate C <-> P: 0.000000 rate C <-> S: 11.133609 rate C <-> T: 3.863205 rate C <-> W: 1.279024 rate C <-> Y: 3.904573 rate C <-> V: 5.107693 rate Q <-> E: 7.930538 rate Q <-> G: 0.185715 rate Q <-> H: 21.395847 rate Q <-> I: 0.435439 rate Q <-> L: 1.721167 rate Q <-> K: 6.672942 rate Q <-> M: 0.966459 rate Q <-> F: 0.193335 rate Q <-> P: 3.638281 rate Q <-> S: 1.762134 rate Q <-> T: 3.389192 rate Q <-> W: 0.000000 rate Q <-> Y: 1.499364 rate Q <-> V: 0.000000 rate E <-> G: 1.974206 rate E <-> H: 0.352278 rate E <-> I: 0.335293 rate E <-> L: 0.358848 rate E <-> K: 3.782919 rate E <-> M: 0.208499 rate E <-> F: 0.217259 rate E <-> P: 0.211251 rate E <-> S: 2.381491 rate E <-> T: 1.942977 rate E <-> W: 0.167965 rate E <-> Y: 0.984052 rate E <-> V: 0.549403 rate G <-> H: 0.699465 rate G <-> I: 0.126175 rate G <-> L: 0.034627 rate G <-> K: 0.386109 rate G <-> M: 0.394329 rate G <-> F: 0.231155 rate G <-> P: 0.199783 rate G <-> S: 6.164468 rate G <-> T: 0.241835 rate G <-> W: 0.970004 rate G <-> Y: 0.000000 rate G <-> V: 0.579148 rate H <-> I: 0.057441 rate H <-> L: 0.971914 rate H <-> K: 0.272808 rate H <-> M: 0.000000 rate H <-> F: 0.644287 rate H <-> P: 0.483728 rate H <-> S: 1.715935 rate H <-> T: 1.328172 rate H <-> W: 0.000000 rate H <-> Y: 11.377727 rate H <-> V: 0.000000 rate I <-> L: 17.918637 rate I <-> K: 1.149476 rate I <-> M: 15.178326 rate I <-> F: 3.233064 rate I <-> P: 0.143749 rate I <-> S: 0.886823 rate I <-> T: 8.201626 rate I <-> W: 0.426502 rate I <-> Y: 1.645174 rate I <-> V: 50.893137 rate L <-> K: 0.639562 rate L <-> M: 13.718808 rate L <-> F: 6.290768 rate L <-> P: 1.026625 rate L <-> S: 1.761715 rate L <-> T: 1.628313 rate L <-> W: 1.432908 rate L <-> Y: 1.104418 rate L <-> V: 4.574604 rate K <-> M: 0.560183 rate K <-> F: 0.116096 rate K <-> P: 0.395515 rate K <-> S: 2.011096 rate K <-> T: 1.810962 rate K <-> W: 0.114852 rate K <-> Y: 0.672534 rate K <-> V: 0.237741 rate M <-> F: 1.782440 rate M <-> P: 0.338178 rate M <-> S: 0.601083 rate M <-> T: 5.024849 rate M <-> W: 0.416902 rate M <-> Y: 0.207986 rate M <-> V: 7.549399 rate F <-> P: 0.272370 rate F <-> S: 1.307870 rate F <-> T: 0.658840 rate F <-> W: 1.172773 rate F <-> Y: 10.889199 rate F <-> V: 1.299940 rate P <-> S: 5.722619 rate P <-> T: 3.022049 rate P <-> W: 0.363853 rate P <-> Y: 0.634153 rate P <-> V: 0.958140 rate S <-> T: 23.453772 rate S <-> W: 0.334299 rate S <-> Y: 1.556855 rate S <-> V: 1.427644 rate T <-> W: 0.137782 rate T <-> Y: 1.119439 rate T <-> V: 11.374566 rate W <-> Y: 2.936643 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 3850.972254 secs or 1.069715 hours Combined Bootstrap and ML search took 6553.035192 secs or 1.820288 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.95perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.95perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-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-PROTGAMMAGTR-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-PROTGAMMAGTR-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-PROTGAMMAGTR-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-PROTGAMMAGTR-supermatrix.mito.full-assemblies.95perc_cov Overall execution time for full ML analysis: 6553.104385 secs or 1.820307 hours or 0.075846 days