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 9294 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 18.81% 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: 9294 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.80perc_cov.fa -n RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.80perc_cov -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 1959.022143 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 107.162250 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 7.547571 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.858914 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.80perc_cov_Partition_No Name Provided Time for BS model parameter optimization 362.669984 Bootstrap[0]: Time 402.539937 seconds, bootstrap likelihood -168429.285856, best rearrangement setting 13 Bootstrap[1]: Time 10.630448 seconds, bootstrap likelihood -168814.782804, best rearrangement setting 13 Bootstrap[2]: Time 38.242629 seconds, bootstrap likelihood -168495.660610, best rearrangement setting 12 Bootstrap[3]: Time 37.542995 seconds, bootstrap likelihood -168345.573226, best rearrangement setting 15 Bootstrap[4]: Time 34.634505 seconds, bootstrap likelihood -170013.072713, best rearrangement setting 10 Bootstrap[5]: Time 35.526076 seconds, bootstrap likelihood -170413.606237, best rearrangement setting 10 Bootstrap[6]: Time 32.064192 seconds, bootstrap likelihood -169468.647321, best rearrangement setting 6 Bootstrap[7]: Time 35.782487 seconds, bootstrap likelihood -170378.088728, best rearrangement setting 14 Bootstrap[8]: Time 31.520531 seconds, bootstrap likelihood -167644.846654, best rearrangement setting 5 Bootstrap[9]: Time 35.024896 seconds, bootstrap likelihood -169499.209516, best rearrangement setting 7 Bootstrap[10]: Time 12.172479 seconds, bootstrap likelihood -170773.999485, best rearrangement setting 7 Bootstrap[11]: Time 11.629271 seconds, bootstrap likelihood -168860.802962, best rearrangement setting 5 Bootstrap[12]: Time 37.017520 seconds, bootstrap likelihood -172156.409156, best rearrangement setting 8 Bootstrap[13]: Time 36.992365 seconds, bootstrap likelihood -169704.446721, best rearrangement setting 7 Bootstrap[14]: Time 37.528704 seconds, bootstrap likelihood -168388.617228, best rearrangement setting 12 Bootstrap[15]: Time 38.172279 seconds, bootstrap likelihood -170881.335070, best rearrangement setting 15 Bootstrap[16]: Time 35.984958 seconds, bootstrap likelihood -168781.190137, best rearrangement setting 12 Bootstrap[17]: Time 36.208365 seconds, bootstrap likelihood -168734.911880, best rearrangement setting 12 Bootstrap[18]: Time 33.724402 seconds, bootstrap likelihood -170714.170518, best rearrangement setting 5 Bootstrap[19]: Time 37.887148 seconds, bootstrap likelihood -168725.805312, best rearrangement setting 8 Bootstrap[20]: Time 38.751520 seconds, bootstrap likelihood -169017.830661, best rearrangement setting 10 Bootstrap[21]: Time 11.988042 seconds, bootstrap likelihood -170897.574525, best rearrangement setting 6 Bootstrap[22]: Time 34.350117 seconds, bootstrap likelihood -168648.854945, best rearrangement setting 5 Bootstrap[23]: Time 35.940056 seconds, bootstrap likelihood -169185.100376, best rearrangement setting 7 Bootstrap[24]: Time 37.818294 seconds, bootstrap likelihood -169744.074566, best rearrangement setting 8 Bootstrap[25]: Time 32.648210 seconds, bootstrap likelihood -169733.089324, best rearrangement setting 6 Bootstrap[26]: Time 37.784943 seconds, bootstrap likelihood -168697.557945, best rearrangement setting 12 Bootstrap[27]: Time 36.796211 seconds, bootstrap likelihood -168751.898108, best rearrangement setting 10 Bootstrap[28]: Time 38.223125 seconds, bootstrap likelihood -168988.658233, best rearrangement setting 11 Bootstrap[29]: Time 36.542998 seconds, bootstrap likelihood -169376.999342, best rearrangement setting 12 Bootstrap[30]: Time 36.656959 seconds, bootstrap likelihood -169113.262913, best rearrangement setting 15 Bootstrap[31]: Time 10.812414 seconds, bootstrap likelihood -169266.239787, best rearrangement setting 15 Bootstrap[32]: Time 34.971777 seconds, bootstrap likelihood -168833.952356, best rearrangement setting 6 Bootstrap[33]: Time 36.728430 seconds, bootstrap likelihood -168858.103350, best rearrangement setting 15 Bootstrap[34]: Time 36.439130 seconds, bootstrap likelihood -168655.074389, best rearrangement setting 11 Bootstrap[35]: Time 34.285976 seconds, bootstrap likelihood -169228.799285, best rearrangement setting 8 Bootstrap[36]: Time 35.549056 seconds, bootstrap likelihood -168308.680267, best rearrangement setting 9 Bootstrap[37]: Time 38.121551 seconds, bootstrap likelihood -167549.787839, best rearrangement setting 11 Bootstrap[38]: Time 36.193061 seconds, bootstrap likelihood -167941.264185, best rearrangement setting 8 Bootstrap[39]: Time 35.550753 seconds, bootstrap likelihood -168309.413251, best rearrangement setting 13 Bootstrap[40]: Time 38.218779 seconds, bootstrap likelihood -170244.603093, best rearrangement setting 13 Bootstrap[41]: Time 36.140894 seconds, bootstrap likelihood -169924.917592, best rearrangement setting 10 Bootstrap[42]: Time 11.651747 seconds, bootstrap likelihood -168978.349885, best rearrangement setting 5 Bootstrap[43]: Time 35.677421 seconds, bootstrap likelihood -168666.985604, best rearrangement setting 14 Bootstrap[44]: Time 36.308953 seconds, bootstrap likelihood -169359.952473, best rearrangement setting 10 Bootstrap[45]: Time 37.427520 seconds, bootstrap likelihood -170449.358373, best rearrangement setting 15 Bootstrap[46]: Time 11.486767 seconds, bootstrap likelihood -170356.081899, best rearrangement setting 14 Bootstrap[47]: Time 36.968415 seconds, bootstrap likelihood -166961.965552, best rearrangement setting 8 Bootstrap[48]: Time 35.076457 seconds, bootstrap likelihood -169035.879939, best rearrangement setting 6 Bootstrap[49]: Time 35.517689 seconds, bootstrap likelihood -168392.093392, best rearrangement setting 7 Bootstrap[50]: Time 35.921549 seconds, bootstrap likelihood -169449.069999, best rearrangement setting 7 Bootstrap[51]: Time 35.081925 seconds, bootstrap likelihood -168135.023279, best rearrangement setting 11 Bootstrap[52]: Time 35.451084 seconds, bootstrap likelihood -169310.879813, best rearrangement setting 12 Bootstrap[53]: Time 37.124309 seconds, bootstrap likelihood -168025.963151, best rearrangement setting 8 Bootstrap[54]: Time 36.104551 seconds, bootstrap likelihood -169084.735258, best rearrangement setting 9 Bootstrap[55]: Time 11.021408 seconds, bootstrap likelihood -169400.093715, best rearrangement setting 11 Bootstrap[56]: Time 10.823600 seconds, bootstrap likelihood -167999.731139, best rearrangement setting 5 Bootstrap[57]: Time 33.807036 seconds, bootstrap likelihood -168356.681047, best rearrangement setting 7 Bootstrap[58]: Time 36.971917 seconds, bootstrap likelihood -169960.398646, best rearrangement setting 10 Bootstrap[59]: Time 34.556501 seconds, bootstrap likelihood -170343.005061, best rearrangement setting 9 Bootstrap[60]: Time 35.199406 seconds, bootstrap likelihood -170043.458320, best rearrangement setting 7 Bootstrap[61]: Time 32.438896 seconds, bootstrap likelihood -167793.298349, best rearrangement setting 5 Bootstrap[62]: Time 37.925655 seconds, bootstrap likelihood -170435.090495, best rearrangement setting 11 Bootstrap[63]: Time 35.314826 seconds, bootstrap likelihood -169310.998310, best rearrangement setting 12 Bootstrap[64]: Time 35.161934 seconds, bootstrap likelihood -168490.072674, best rearrangement setting 7 Bootstrap[65]: Time 33.474157 seconds, bootstrap likelihood -168617.309078, best rearrangement setting 5 Bootstrap[66]: Time 33.645929 seconds, bootstrap likelihood -169388.623536, best rearrangement setting 5 Bootstrap[67]: Time 35.591301 seconds, bootstrap likelihood -168742.266249, best rearrangement setting 15 Bootstrap[68]: Time 39.001316 seconds, bootstrap likelihood -170186.430797, best rearrangement setting 11 Bootstrap[69]: Time 32.950903 seconds, bootstrap likelihood -167494.608295, best rearrangement setting 5 Bootstrap[70]: Time 36.653259 seconds, bootstrap likelihood -168517.792718, best rearrangement setting 8 Bootstrap[71]: Time 36.814957 seconds, bootstrap likelihood -170317.401924, best rearrangement setting 10 Bootstrap[72]: Time 35.864806 seconds, bootstrap likelihood -170945.513183, best rearrangement setting 11 Bootstrap[73]: Time 40.186802 seconds, bootstrap likelihood -168769.580306, best rearrangement setting 9 Bootstrap[74]: Time 33.540268 seconds, bootstrap likelihood -170680.066240, best rearrangement setting 5 Bootstrap[75]: Time 38.319447 seconds, bootstrap likelihood -170106.569358, best rearrangement setting 8 Bootstrap[76]: Time 37.013152 seconds, bootstrap likelihood -168614.036144, best rearrangement setting 9 Bootstrap[77]: Time 36.911576 seconds, bootstrap likelihood -169613.358702, best rearrangement setting 11 Bootstrap[78]: Time 37.159499 seconds, bootstrap likelihood -170188.178591, best rearrangement setting 15 Bootstrap[79]: Time 10.477582 seconds, bootstrap likelihood -167413.495784, best rearrangement setting 9 Bootstrap[80]: Time 36.972809 seconds, bootstrap likelihood -169960.161012, best rearrangement setting 15 Bootstrap[81]: Time 37.714496 seconds, bootstrap likelihood -167675.137272, best rearrangement setting 7 Bootstrap[82]: Time 35.135448 seconds, bootstrap likelihood -168815.748849, best rearrangement setting 6 Bootstrap[83]: Time 36.939528 seconds, bootstrap likelihood -169810.006345, best rearrangement setting 10 Bootstrap[84]: Time 35.988261 seconds, bootstrap likelihood -168201.644630, best rearrangement setting 11 Bootstrap[85]: Time 37.659195 seconds, bootstrap likelihood -169221.248175, best rearrangement setting 8 Bootstrap[86]: Time 33.887020 seconds, bootstrap likelihood -168301.892538, best rearrangement setting 7 Bootstrap[87]: Time 36.790145 seconds, bootstrap likelihood -169814.883007, best rearrangement setting 7 Bootstrap[88]: Time 37.310421 seconds, bootstrap likelihood -168246.161440, best rearrangement setting 12 Bootstrap[89]: Time 37.880369 seconds, bootstrap likelihood -168541.084824, best rearrangement setting 10 Bootstrap[90]: Time 35.733182 seconds, bootstrap likelihood -169216.240717, best rearrangement setting 8 Bootstrap[91]: Time 37.564738 seconds, bootstrap likelihood -168499.408416, best rearrangement setting 12 Bootstrap[92]: Time 36.751138 seconds, bootstrap likelihood -169840.516212, best rearrangement setting 13 Bootstrap[93]: Time 37.962664 seconds, bootstrap likelihood -168995.209028, best rearrangement setting 15 Bootstrap[94]: Time 30.610278 seconds, bootstrap likelihood -169584.066532, best rearrangement setting 5 Bootstrap[95]: Time 33.808245 seconds, bootstrap likelihood -167817.868210, best rearrangement setting 5 Bootstrap[96]: Time 36.924475 seconds, bootstrap likelihood -168229.123078, best rearrangement setting 13 Bootstrap[97]: Time 37.910622 seconds, bootstrap likelihood -169669.291174, best rearrangement setting 11 Bootstrap[98]: Time 10.130662 seconds, bootstrap likelihood -169224.866985, best rearrangement setting 6 Bootstrap[99]: Time 37.006629 seconds, bootstrap likelihood -168793.976264, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 3703.065623 seconds Average Time per Rapid Bootstrap 37.030656 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 1960.497005 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 107.382067 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 7.579880 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.862995 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.137789 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.032829 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.80perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 2807.899253 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1960.241307 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 107.150678 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 7.546461 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.856610 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.137178 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.032859 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.80perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -169134.375511 Slow ML Search 1 Likelihood: -169134.375510 Slow ML Search 2 Likelihood: -169134.375509 Slow ML Search 3 Likelihood: -169134.375509 Slow ML Search 4 Likelihood: -169134.375511 Slow ML Search 5 Likelihood: -169134.375511 Slow ML Search 6 Likelihood: -169134.375509 Slow ML Search 7 Likelihood: -169134.375509 Slow ML Search 8 Likelihood: -169134.375511 Slow ML Search 9 Likelihood: -169134.375511 Slow ML optimization finished Slow ML search Time: 1747.373359 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1960.169894 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 107.136643 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 7.569648 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.867963 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.140259 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.033541 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.80perc_cov_Partition_No Name Provided Thorough ML search Time: 695.247024 seconds Final ML Optimization Likelihood: -169134.364250 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.658642 Tree-Length: 19.353361 rate A <-> R: 0.379484 rate A <-> N: 0.475173 rate A <-> D: 2.897766 rate A <-> C: 6.815972 rate A <-> Q: 0.677236 rate A <-> E: 3.003091 rate A <-> G: 7.582077 rate A <-> H: 0.513672 rate A <-> I: 2.003195 rate A <-> L: 1.538619 rate A <-> K: 0.251036 rate A <-> M: 1.773295 rate A <-> F: 0.925927 rate A <-> P: 4.789683 rate A <-> S: 22.763596 rate A <-> T: 15.486912 rate A <-> W: 0.139296 rate A <-> Y: 0.052785 rate A <-> V: 14.284707 rate R <-> N: 0.477916 rate R <-> D: 0.012330 rate R <-> C: 1.276143 rate R <-> Q: 5.858313 rate R <-> E: 1.022601 rate R <-> G: 1.398048 rate R <-> H: 4.521623 rate R <-> I: 0.299239 rate R <-> L: 0.456084 rate R <-> K: 21.165014 rate R <-> M: 1.143125 rate R <-> F: 0.111516 rate R <-> P: 0.545630 rate R <-> S: 1.208751 rate R <-> T: 0.738966 rate R <-> W: 1.156920 rate R <-> Y: 0.427888 rate R <-> V: 0.000000 rate N <-> D: 14.471800 rate N <-> C: 0.868357 rate N <-> Q: 6.849413 rate N <-> E: 3.242091 rate N <-> G: 2.469589 rate N <-> H: 8.244412 rate N <-> I: 2.539166 rate N <-> L: 0.907312 rate N <-> K: 8.373848 rate N <-> M: 0.663062 rate N <-> F: 0.579970 rate N <-> P: 0.434484 rate N <-> S: 14.966283 rate N <-> T: 8.684606 rate N <-> W: 0.205221 rate N <-> Y: 3.625906 rate N <-> V: 0.274375 rate D <-> C: 0.985094 rate D <-> Q: 0.000000 rate D <-> E: 31.764591 rate D <-> G: 2.777158 rate D <-> H: 1.820244 rate D <-> I: 0.112894 rate D <-> L: 0.155289 rate D <-> K: 1.101093 rate D <-> M: 0.000000 rate D <-> F: 0.136290 rate D <-> P: 1.187601 rate D <-> S: 3.485030 rate D <-> T: 1.649647 rate D <-> W: 0.191406 rate D <-> Y: 0.496641 rate D <-> V: 0.488995 rate C <-> Q: 0.184576 rate C <-> E: 0.000000 rate C <-> G: 2.986679 rate C <-> H: 3.228822 rate C <-> I: 1.229038 rate C <-> L: 1.496498 rate C <-> K: 0.000000 rate C <-> M: 2.344710 rate C <-> F: 1.779777 rate C <-> P: 0.000000 rate C <-> S: 9.906473 rate C <-> T: 3.526695 rate C <-> W: 1.516251 rate C <-> Y: 5.077717 rate C <-> V: 4.869174 rate Q <-> E: 7.968588 rate Q <-> G: 0.109335 rate Q <-> H: 23.295326 rate Q <-> I: 0.586296 rate Q <-> L: 1.611354 rate Q <-> K: 7.217697 rate Q <-> M: 1.835569 rate Q <-> F: 0.309027 rate Q <-> P: 4.058752 rate Q <-> S: 2.138016 rate Q <-> T: 2.827409 rate Q <-> W: 0.000000 rate Q <-> Y: 1.541357 rate Q <-> V: 0.161580 rate E <-> G: 3.273959 rate E <-> H: 1.438825 rate E <-> I: 0.301592 rate E <-> L: 0.400694 rate E <-> K: 3.971838 rate E <-> M: 0.098357 rate E <-> F: 0.124793 rate E <-> P: 0.912592 rate E <-> S: 2.337815 rate E <-> T: 1.874086 rate E <-> W: 0.160390 rate E <-> Y: 0.696567 rate E <-> V: 1.081076 rate G <-> H: 0.581413 rate G <-> I: 0.127900 rate G <-> L: 0.039315 rate G <-> K: 0.374633 rate G <-> M: 0.431504 rate G <-> F: 0.262019 rate G <-> P: 0.255300 rate G <-> S: 6.635897 rate G <-> T: 0.657714 rate G <-> W: 1.015643 rate G <-> Y: 0.000000 rate G <-> V: 0.785139 rate H <-> I: 0.211371 rate H <-> L: 0.830376 rate H <-> K: 0.484221 rate H <-> M: 0.000000 rate H <-> F: 0.552518 rate H <-> P: 1.025202 rate H <-> S: 1.790468 rate H <-> T: 1.548991 rate H <-> W: 0.000000 rate H <-> Y: 12.623192 rate H <-> V: 0.000000 rate I <-> L: 17.435438 rate I <-> K: 1.357345 rate I <-> M: 16.083751 rate I <-> F: 3.356770 rate I <-> P: 0.108046 rate I <-> S: 1.075756 rate I <-> T: 8.509013 rate I <-> W: 0.430899 rate I <-> Y: 2.240709 rate I <-> V: 48.572509 rate L <-> K: 0.559093 rate L <-> M: 13.579683 rate L <-> F: 6.097315 rate L <-> P: 1.117423 rate L <-> S: 1.773356 rate L <-> T: 1.780856 rate L <-> W: 1.395718 rate L <-> Y: 1.285147 rate L <-> V: 4.903981 rate K <-> M: 0.490021 rate K <-> F: 0.124820 rate K <-> P: 0.488983 rate K <-> S: 2.022976 rate K <-> T: 1.875092 rate K <-> W: 0.098983 rate K <-> Y: 0.772531 rate K <-> V: 0.266323 rate M <-> F: 1.565227 rate M <-> P: 0.226128 rate M <-> S: 0.611569 rate M <-> T: 5.202264 rate M <-> W: 0.437108 rate M <-> Y: 0.634586 rate M <-> V: 7.708364 rate F <-> P: 0.269903 rate F <-> S: 1.319538 rate F <-> T: 0.682316 rate F <-> W: 1.344504 rate F <-> Y: 10.320077 rate F <-> V: 1.396519 rate P <-> S: 6.319097 rate P <-> T: 3.453969 rate P <-> W: 0.310590 rate P <-> Y: 0.860957 rate P <-> V: 1.486917 rate S <-> T: 22.392517 rate S <-> W: 0.329770 rate S <-> Y: 1.630321 rate S <-> V: 1.557750 rate T <-> W: 0.079205 rate T <-> Y: 0.868720 rate T <-> V: 11.661369 rate W <-> Y: 2.846092 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.043245 freq pi(R): 0.037119 freq pi(N): 0.064533 freq pi(D): 0.028844 freq pi(C): 0.012327 freq pi(Q): 0.017449 freq pi(E): 0.035517 freq pi(G): 0.039518 freq pi(H): 0.016911 freq pi(I): 0.074689 freq pi(L): 0.123516 freq pi(K): 0.080776 freq pi(M): 0.017389 freq pi(F): 0.141912 freq pi(P): 0.021621 freq pi(S): 0.074494 freq pi(T): 0.045034 freq pi(W): 0.015501 freq pi(Y): 0.054199 freq pi(V): 0.055404 ML search took 5250.616436 secs or 1.458505 hours Combined Bootstrap and ML search took 8953.682886 secs or 2.487134 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.80perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.80perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.80perc_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.80perc_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.80perc_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.80perc_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.80perc_cov Overall execution time for full ML analysis: 8953.764191 secs or 2.487157 hours or 0.103632 days