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 8542 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 18.01% 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: 8542 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.90perc_cov.fa -n RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.90perc_cov -m PROTCATGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 12204.135888 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2579.287677 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 139.637192 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.488546 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.90perc_cov_Partition_No Name Provided Time for BS model parameter optimization 136.787623 Bootstrap[0]: Time 145.832072 seconds, bootstrap likelihood -144376.874236, best rearrangement setting 13 Bootstrap[1]: Time 8.326256 seconds, bootstrap likelihood -144860.621820, best rearrangement setting 13 Bootstrap[2]: Time 2.714981 seconds, bootstrap likelihood -146047.434661, best rearrangement setting 12 Bootstrap[3]: Time 2.687546 seconds, bootstrap likelihood -146982.009332, best rearrangement setting 15 Bootstrap[4]: Time 7.997473 seconds, bootstrap likelihood -144960.214344, best rearrangement setting 10 Bootstrap[5]: Time 8.079302 seconds, bootstrap likelihood -145330.378680, best rearrangement setting 10 Bootstrap[6]: Time 7.837323 seconds, bootstrap likelihood -143796.929223, best rearrangement setting 6 Bootstrap[7]: Time 8.029263 seconds, bootstrap likelihood -145779.459870, best rearrangement setting 14 Bootstrap[8]: Time 8.092822 seconds, bootstrap likelihood -146175.825493, best rearrangement setting 5 Bootstrap[9]: Time 2.689665 seconds, bootstrap likelihood -145331.988568, best rearrangement setting 7 Bootstrap[10]: Time 8.311055 seconds, bootstrap likelihood -146511.383188, best rearrangement setting 7 Bootstrap[11]: Time 7.845047 seconds, bootstrap likelihood -145945.995436, best rearrangement setting 5 Bootstrap[12]: Time 2.784793 seconds, bootstrap likelihood -144847.661388, best rearrangement setting 8 Bootstrap[13]: Time 2.743856 seconds, bootstrap likelihood -147055.777356, best rearrangement setting 7 Bootstrap[14]: Time 8.137083 seconds, bootstrap likelihood -146825.378420, best rearrangement setting 12 Bootstrap[15]: Time 8.566816 seconds, bootstrap likelihood -145710.902382, best rearrangement setting 15 Bootstrap[16]: Time 2.779976 seconds, bootstrap likelihood -146291.601702, best rearrangement setting 12 Bootstrap[17]: Time 2.780278 seconds, bootstrap likelihood -145341.064229, best rearrangement setting 12 Bootstrap[18]: Time 2.868233 seconds, bootstrap likelihood -145062.893727, best rearrangement setting 5 Bootstrap[19]: Time 2.852135 seconds, bootstrap likelihood -145461.279392, best rearrangement setting 8 Bootstrap[20]: Time 8.818762 seconds, bootstrap likelihood -146540.438378, best rearrangement setting 10 Bootstrap[21]: Time 8.596712 seconds, bootstrap likelihood -144506.024082, best rearrangement setting 6 Bootstrap[22]: Time 7.731134 seconds, bootstrap likelihood -146815.949783, best rearrangement setting 5 Bootstrap[23]: Time 8.584290 seconds, bootstrap likelihood -146640.495715, best rearrangement setting 7 Bootstrap[24]: Time 8.146473 seconds, bootstrap likelihood -146534.285050, best rearrangement setting 8 Bootstrap[25]: Time 2.655454 seconds, bootstrap likelihood -144718.803551, best rearrangement setting 6 Bootstrap[26]: Time 2.751234 seconds, bootstrap likelihood -145809.252628, best rearrangement setting 12 Bootstrap[27]: Time 2.649398 seconds, bootstrap likelihood -146030.577809, best rearrangement setting 10 Bootstrap[28]: Time 8.041361 seconds, bootstrap likelihood -145511.139158, best rearrangement setting 11 Bootstrap[29]: Time 2.683634 seconds, bootstrap likelihood -144804.046485, best rearrangement setting 12 Bootstrap[30]: Time 3.020570 seconds, bootstrap likelihood -144760.023332, best rearrangement setting 15 Bootstrap[31]: Time 2.836278 seconds, bootstrap likelihood -146136.752169, best rearrangement setting 15 Bootstrap[32]: Time 8.010065 seconds, bootstrap likelihood -145152.648575, best rearrangement setting 6 Bootstrap[33]: Time 8.236797 seconds, bootstrap likelihood -145265.890243, best rearrangement setting 15 Bootstrap[34]: Time 8.675894 seconds, bootstrap likelihood -143737.396639, best rearrangement setting 11 Bootstrap[35]: Time 7.844243 seconds, bootstrap likelihood -145499.768899, best rearrangement setting 8 Bootstrap[36]: Time 8.041782 seconds, bootstrap likelihood -144436.616316, best rearrangement setting 9 Bootstrap[37]: Time 8.310196 seconds, bootstrap likelihood -145054.010998, best rearrangement setting 11 Bootstrap[38]: Time 8.109385 seconds, bootstrap likelihood -146427.831963, best rearrangement setting 8 Bootstrap[39]: Time 8.333822 seconds, bootstrap likelihood -145882.816687, best rearrangement setting 13 Bootstrap[40]: Time 8.133142 seconds, bootstrap likelihood -145796.272351, best rearrangement setting 13 Bootstrap[41]: Time 2.813814 seconds, bootstrap likelihood -145115.682098, best rearrangement setting 10 Bootstrap[42]: Time 2.671518 seconds, bootstrap likelihood -145681.452214, best rearrangement setting 5 Bootstrap[43]: Time 8.502507 seconds, bootstrap likelihood -146885.679158, best rearrangement setting 14 Bootstrap[44]: Time 8.157557 seconds, bootstrap likelihood -146453.859681, best rearrangement setting 10 Bootstrap[45]: Time 8.127887 seconds, bootstrap likelihood -145807.031661, best rearrangement setting 15 Bootstrap[46]: Time 8.595055 seconds, bootstrap likelihood -145393.303351, best rearrangement setting 14 Bootstrap[47]: Time 2.955567 seconds, bootstrap likelihood -145139.797023, best rearrangement setting 8 Bootstrap[48]: Time 2.830920 seconds, bootstrap likelihood -146272.292088, best rearrangement setting 6 Bootstrap[49]: Time 2.817288 seconds, bootstrap likelihood -146340.255220, best rearrangement setting 7 Bootstrap[50]: Time 3.018668 seconds, bootstrap likelihood -146093.813062, best rearrangement setting 7 Bootstrap[51]: Time 2.769979 seconds, bootstrap likelihood -145152.541064, best rearrangement setting 11 Bootstrap[52]: Time 8.276915 seconds, bootstrap likelihood -144869.503475, best rearrangement setting 12 Bootstrap[53]: Time 8.308700 seconds, bootstrap likelihood -147290.009877, best rearrangement setting 8 Bootstrap[54]: Time 2.750366 seconds, bootstrap likelihood -146026.964673, best rearrangement setting 9 Bootstrap[55]: Time 2.737148 seconds, bootstrap likelihood -145347.939017, best rearrangement setting 11 Bootstrap[56]: Time 7.650664 seconds, bootstrap likelihood -145584.255828, best rearrangement setting 5 Bootstrap[57]: Time 8.364599 seconds, bootstrap likelihood -146441.058565, best rearrangement setting 7 Bootstrap[58]: Time 2.849595 seconds, bootstrap likelihood -145150.418261, best rearrangement setting 10 Bootstrap[59]: Time 8.059705 seconds, bootstrap likelihood -146352.385524, best rearrangement setting 9 Bootstrap[60]: Time 2.951645 seconds, bootstrap likelihood -145904.985742, best rearrangement setting 7 Bootstrap[61]: Time 7.655594 seconds, bootstrap likelihood -143578.200455, best rearrangement setting 5 Bootstrap[62]: Time 9.087887 seconds, bootstrap likelihood -147178.225069, best rearrangement setting 11 Bootstrap[63]: Time 8.873614 seconds, bootstrap likelihood -145177.476468, best rearrangement setting 12 Bootstrap[64]: Time 2.700818 seconds, bootstrap likelihood -146664.640114, best rearrangement setting 7 Bootstrap[65]: Time 7.554258 seconds, bootstrap likelihood -145575.012131, best rearrangement setting 5 Bootstrap[66]: Time 7.395279 seconds, bootstrap likelihood -143624.410939, best rearrangement setting 5 Bootstrap[67]: Time 8.239612 seconds, bootstrap likelihood -146361.386320, best rearrangement setting 15 Bootstrap[68]: Time 8.400867 seconds, bootstrap likelihood -145544.822383, best rearrangement setting 11 Bootstrap[69]: Time 7.703804 seconds, bootstrap likelihood -144534.624440, best rearrangement setting 5 Bootstrap[70]: Time 3.235926 seconds, bootstrap likelihood -145906.814964, best rearrangement setting 8 Bootstrap[71]: Time 2.961107 seconds, bootstrap likelihood -146319.673506, best rearrangement setting 10 Bootstrap[72]: Time 8.301821 seconds, bootstrap likelihood -145792.778014, best rearrangement setting 11 Bootstrap[73]: Time 8.101109 seconds, bootstrap likelihood -145679.738214, best rearrangement setting 9 Bootstrap[74]: Time 7.606777 seconds, bootstrap likelihood -145321.937928, best rearrangement setting 5 Bootstrap[75]: Time 8.208469 seconds, bootstrap likelihood -146695.479261, best rearrangement setting 8 Bootstrap[76]: Time 8.258021 seconds, bootstrap likelihood -144955.663461, best rearrangement setting 9 Bootstrap[77]: Time 8.449308 seconds, bootstrap likelihood -145824.360007, best rearrangement setting 11 Bootstrap[78]: Time 7.962876 seconds, bootstrap likelihood -145637.680168, best rearrangement setting 15 Bootstrap[79]: Time 8.544594 seconds, bootstrap likelihood -145538.474047, best rearrangement setting 9 Bootstrap[80]: Time 3.060665 seconds, bootstrap likelihood -147397.833444, best rearrangement setting 15 Bootstrap[81]: Time 7.950013 seconds, bootstrap likelihood -144927.166523, best rearrangement setting 7 Bootstrap[82]: Time 7.776332 seconds, bootstrap likelihood -144759.953903, best rearrangement setting 6 Bootstrap[83]: Time 8.266480 seconds, bootstrap likelihood -145616.067300, best rearrangement setting 10 Bootstrap[84]: Time 8.352016 seconds, bootstrap likelihood -146663.405726, best rearrangement setting 11 Bootstrap[85]: Time 2.931056 seconds, bootstrap likelihood -144381.337832, best rearrangement setting 8 Bootstrap[86]: Time 2.833511 seconds, bootstrap likelihood -144474.965347, best rearrangement setting 7 Bootstrap[87]: Time 8.094149 seconds, bootstrap likelihood -144356.781350, best rearrangement setting 7 Bootstrap[88]: Time 8.567416 seconds, bootstrap likelihood -145191.713215, best rearrangement setting 12 Bootstrap[89]: Time 8.380981 seconds, bootstrap likelihood -144200.974453, best rearrangement setting 10 Bootstrap[90]: Time 2.960327 seconds, bootstrap likelihood -144624.102303, best rearrangement setting 8 Bootstrap[91]: Time 8.366566 seconds, bootstrap likelihood -144939.389665, best rearrangement setting 12 Bootstrap[92]: Time 8.001024 seconds, bootstrap likelihood -146641.379142, best rearrangement setting 13 Bootstrap[93]: Time 2.742826 seconds, bootstrap likelihood -144464.285230, best rearrangement setting 15 Bootstrap[94]: Time 2.781733 seconds, bootstrap likelihood -144942.939945, best rearrangement setting 5 Bootstrap[95]: Time 7.852043 seconds, bootstrap likelihood -145635.222719, best rearrangement setting 5 Bootstrap[96]: Time 8.142861 seconds, bootstrap likelihood -144596.778899, best rearrangement setting 13 Bootstrap[97]: Time 8.384600 seconds, bootstrap likelihood -145646.391129, best rearrangement setting 11 Bootstrap[98]: Time 2.729679 seconds, bootstrap likelihood -145138.309449, best rearrangement setting 6 Bootstrap[99]: Time 8.322564 seconds, bootstrap likelihood -145588.470778, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 763.501040 seconds Average Time per Rapid Bootstrap 7.635010 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 1917.523726 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 90.865625 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.976799 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.251591 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.015770 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.90perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 628.523765 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1917.542898 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 90.843929 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.975097 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.251465 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.015759 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1802.198571 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 89.929212 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.449409 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.533396 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.083727 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.90perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -153724.840413 Slow ML Search 1 Likelihood: -153724.839614 Slow ML Search 2 Likelihood: -153724.827923 Slow ML Search 3 Likelihood: -153724.832012 Slow ML Search 4 Likelihood: -153724.825702 Slow ML Search 5 Likelihood: -153724.825702 Slow ML Search 6 Likelihood: -153724.826789 Slow ML Search 7 Likelihood: -153724.825706 Slow ML Search 8 Likelihood: -153724.839717 Slow ML Search 9 Likelihood: -153724.840168 Slow ML optimization finished Slow ML search Time: 898.093138 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1802.173282 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 89.880197 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.440873 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.533664 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.083940 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.90perc_cov_Partition_No Name Provided Thorough ML search Time: 551.892567 seconds Final ML Optimization Likelihood: -153724.832497 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.692613 Tree-Length: 17.021318 rate A <-> R: 0.368306 rate A <-> N: 0.562665 rate A <-> D: 1.881864 rate A <-> C: 7.330233 rate A <-> Q: 0.171268 rate A <-> E: 2.338052 rate A <-> G: 6.396839 rate A <-> H: 0.386865 rate A <-> I: 1.875581 rate A <-> L: 1.454848 rate A <-> K: 0.148791 rate A <-> M: 1.944273 rate A <-> F: 0.980825 rate A <-> P: 4.136749 rate A <-> S: 22.977286 rate A <-> T: 14.618661 rate A <-> W: 0.171611 rate A <-> Y: 0.000000 rate A <-> V: 14.040876 rate R <-> N: 0.615308 rate R <-> D: 0.000000 rate R <-> C: 1.012283 rate R <-> Q: 5.278965 rate R <-> E: 0.688147 rate R <-> G: 1.100517 rate R <-> H: 4.221151 rate R <-> I: 0.295603 rate R <-> L: 0.400028 rate R <-> K: 21.765836 rate R <-> M: 1.167621 rate R <-> F: 0.105013 rate R <-> P: 0.308539 rate R <-> S: 1.257676 rate R <-> T: 0.714742 rate R <-> W: 1.081061 rate R <-> Y: 0.352633 rate R <-> V: 0.000000 rate N <-> D: 14.431132 rate N <-> C: 0.828445 rate N <-> Q: 7.263757 rate N <-> E: 3.519470 rate N <-> G: 2.483822 rate N <-> H: 8.632847 rate N <-> I: 2.436245 rate N <-> L: 0.946636 rate N <-> K: 8.376267 rate N <-> M: 0.768713 rate N <-> F: 0.567443 rate N <-> P: 0.468516 rate N <-> S: 14.978573 rate N <-> T: 9.017119 rate N <-> W: 0.258163 rate N <-> Y: 3.864884 rate N <-> V: 0.331951 rate D <-> C: 0.885684 rate D <-> Q: 0.000000 rate D <-> E: 30.320399 rate D <-> G: 2.107792 rate D <-> H: 2.144558 rate D <-> I: 0.107139 rate D <-> L: 0.077646 rate D <-> K: 0.844866 rate D <-> M: 0.000000 rate D <-> F: 0.081269 rate D <-> P: 0.932459 rate D <-> S: 3.421791 rate D <-> T: 1.105276 rate D <-> W: 0.210641 rate D <-> Y: 0.467363 rate D <-> V: 0.359174 rate C <-> Q: 0.212824 rate C <-> E: 0.079123 rate C <-> G: 2.344517 rate C <-> H: 3.478455 rate C <-> I: 1.329668 rate C <-> L: 1.490083 rate C <-> K: 0.000000 rate C <-> M: 2.462411 rate C <-> F: 1.799967 rate C <-> P: 0.000000 rate C <-> S: 10.325360 rate C <-> T: 3.700905 rate C <-> W: 1.591217 rate C <-> Y: 4.360939 rate C <-> V: 4.890726 rate Q <-> E: 7.626709 rate Q <-> G: 0.138421 rate Q <-> H: 20.270237 rate Q <-> I: 0.555732 rate Q <-> L: 1.538656 rate Q <-> K: 7.007465 rate Q <-> M: 1.579816 rate Q <-> F: 0.308937 rate Q <-> P: 3.477888 rate Q <-> S: 2.250117 rate Q <-> T: 3.249240 rate Q <-> W: 0.000000 rate Q <-> Y: 1.237455 rate Q <-> V: 0.000000 rate E <-> G: 1.894114 rate E <-> H: 0.272658 rate E <-> I: 0.351123 rate E <-> L: 0.367534 rate E <-> K: 3.777960 rate E <-> M: 0.167301 rate E <-> F: 0.147002 rate E <-> P: 0.358685 rate E <-> S: 2.375175 rate E <-> T: 1.748911 rate E <-> W: 0.153202 rate E <-> Y: 0.857248 rate E <-> V: 0.656395 rate G <-> H: 0.625644 rate G <-> I: 0.109975 rate G <-> L: 0.025595 rate G <-> K: 0.421540 rate G <-> M: 0.373503 rate G <-> F: 0.248280 rate G <-> P: 0.289226 rate G <-> S: 6.156556 rate G <-> T: 0.469636 rate G <-> W: 0.831936 rate G <-> Y: 0.000000 rate G <-> V: 0.622899 rate H <-> I: 0.142128 rate H <-> L: 0.871765 rate H <-> K: 0.382183 rate H <-> M: 0.000000 rate H <-> F: 0.617317 rate H <-> P: 0.461106 rate H <-> S: 1.878718 rate H <-> T: 1.239717 rate H <-> W: 0.000000 rate H <-> Y: 11.847807 rate H <-> V: 0.000000 rate I <-> L: 17.816224 rate I <-> K: 1.298755 rate I <-> M: 15.549084 rate I <-> F: 3.389266 rate I <-> P: 0.127339 rate I <-> S: 1.076393 rate I <-> T: 8.325392 rate I <-> W: 0.498644 rate I <-> Y: 2.227173 rate I <-> V: 49.009836 rate L <-> K: 0.522822 rate L <-> M: 13.498252 rate L <-> F: 6.223165 rate L <-> P: 1.024350 rate L <-> S: 1.764029 rate L <-> T: 1.621521 rate L <-> W: 1.373979 rate L <-> Y: 1.289009 rate L <-> V: 5.121240 rate K <-> M: 0.496165 rate K <-> F: 0.132824 rate K <-> P: 0.391756 rate K <-> S: 2.029094 rate K <-> T: 1.813578 rate K <-> W: 0.085409 rate K <-> Y: 0.745569 rate K <-> V: 0.238379 rate M <-> F: 1.611891 rate M <-> P: 0.292036 rate M <-> S: 0.665218 rate M <-> T: 5.074224 rate M <-> W: 0.410092 rate M <-> Y: 0.729918 rate M <-> V: 7.924949 rate F <-> P: 0.239056 rate F <-> S: 1.302414 rate F <-> T: 0.625225 rate F <-> W: 1.187150 rate F <-> Y: 10.693123 rate F <-> V: 1.405616 rate P <-> S: 6.011293 rate P <-> T: 3.227822 rate P <-> W: 0.345665 rate P <-> Y: 0.812051 rate P <-> V: 1.223358 rate S <-> T: 22.190469 rate S <-> W: 0.285695 rate S <-> Y: 1.612080 rate S <-> V: 1.431015 rate T <-> W: 0.099243 rate T <-> Y: 0.850608 rate T <-> V: 11.992441 rate W <-> Y: 2.817640 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.042992 freq pi(R): 0.037329 freq pi(N): 0.064214 freq pi(D): 0.027285 freq pi(C): 0.012716 freq pi(Q): 0.017124 freq pi(E): 0.032780 freq pi(G): 0.039908 freq pi(H): 0.016974 freq pi(I): 0.076278 freq pi(L): 0.123454 freq pi(K): 0.079995 freq pi(M): 0.017975 freq pi(F): 0.142980 freq pi(P): 0.020807 freq pi(S): 0.074742 freq pi(T): 0.045922 freq pi(W): 0.015803 freq pi(Y): 0.054803 freq pi(V): 0.055919 ML search took 2078.599839 secs or 0.577389 hours Combined Bootstrap and ML search took 2842.101682 secs or 0.789473 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.90perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.90perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.90perc_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.90perc_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.90perc_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.90perc_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.90perc_cov Overall execution time for full ML analysis: 2842.186386 secs or 0.789496 hours or 0.032896 days