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 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: 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-PROTGAMMAGTR-supermatrix.mito.full-assemblies.90perc_cov -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 1801.823716 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 89.817737 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.436354 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.534041 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.90perc_cov_Partition_No Name Provided Time for BS model parameter optimization 335.429945 Bootstrap[0]: Time 369.025598 seconds, bootstrap likelihood -152433.746698, best rearrangement setting 13 Bootstrap[1]: Time 34.649299 seconds, bootstrap likelihood -152917.636300, best rearrangement setting 13 Bootstrap[2]: Time 33.213907 seconds, bootstrap likelihood -154182.595034, best rearrangement setting 12 Bootstrap[3]: Time 33.525839 seconds, bootstrap likelihood -155056.085676, best rearrangement setting 15 Bootstrap[4]: Time 31.912307 seconds, bootstrap likelihood -153075.774943, best rearrangement setting 10 Bootstrap[5]: Time 32.580474 seconds, bootstrap likelihood -153410.157095, best rearrangement setting 10 Bootstrap[6]: Time 9.267191 seconds, bootstrap likelihood -151726.547367, best rearrangement setting 6 Bootstrap[7]: Time 34.113704 seconds, bootstrap likelihood -153819.987396, best rearrangement setting 14 Bootstrap[8]: Time 30.219168 seconds, bootstrap likelihood -154265.419389, best rearrangement setting 5 Bootstrap[9]: Time 32.787969 seconds, bootstrap likelihood -153322.565800, best rearrangement setting 7 Bootstrap[10]: Time 30.747170 seconds, bootstrap likelihood -154543.525553, best rearrangement setting 7 Bootstrap[11]: Time 31.606112 seconds, bootstrap likelihood -154039.417237, best rearrangement setting 5 Bootstrap[12]: Time 32.210003 seconds, bootstrap likelihood -152913.419074, best rearrangement setting 8 Bootstrap[13]: Time 31.774387 seconds, bootstrap likelihood -155257.145908, best rearrangement setting 7 Bootstrap[14]: Time 32.542627 seconds, bootstrap likelihood -154940.139109, best rearrangement setting 12 Bootstrap[15]: Time 33.886276 seconds, bootstrap likelihood -153838.745410, best rearrangement setting 15 Bootstrap[16]: Time 9.685252 seconds, bootstrap likelihood -154396.974725, best rearrangement setting 12 Bootstrap[17]: Time 10.157963 seconds, bootstrap likelihood -153359.596493, best rearrangement setting 12 Bootstrap[18]: Time 10.662376 seconds, bootstrap likelihood -153120.383720, best rearrangement setting 5 Bootstrap[19]: Time 10.275374 seconds, bootstrap likelihood -153654.469059, best rearrangement setting 8 Bootstrap[20]: Time 10.500361 seconds, bootstrap likelihood -154654.657995, best rearrangement setting 10 Bootstrap[21]: Time 32.520957 seconds, bootstrap likelihood -152653.882091, best rearrangement setting 6 Bootstrap[22]: Time 31.200987 seconds, bootstrap likelihood -155016.478511, best rearrangement setting 5 Bootstrap[23]: Time 32.376579 seconds, bootstrap likelihood -154738.880854, best rearrangement setting 7 Bootstrap[24]: Time 10.597813 seconds, bootstrap likelihood -154657.512625, best rearrangement setting 8 Bootstrap[25]: Time 30.349251 seconds, bootstrap likelihood -152645.984511, best rearrangement setting 6 Bootstrap[26]: Time 34.017915 seconds, bootstrap likelihood -153984.911113, best rearrangement setting 12 Bootstrap[27]: Time 9.339434 seconds, bootstrap likelihood -154113.719594, best rearrangement setting 10 Bootstrap[28]: Time 32.472756 seconds, bootstrap likelihood -153633.773768, best rearrangement setting 11 Bootstrap[29]: Time 30.788907 seconds, bootstrap likelihood -152884.501728, best rearrangement setting 12 Bootstrap[30]: Time 10.106980 seconds, bootstrap likelihood -152828.590400, best rearrangement setting 15 Bootstrap[31]: Time 11.066775 seconds, bootstrap likelihood -154218.393075, best rearrangement setting 15 Bootstrap[32]: Time 30.183007 seconds, bootstrap likelihood -153201.248633, best rearrangement setting 6 Bootstrap[33]: Time 32.501700 seconds, bootstrap likelihood -153332.848588, best rearrangement setting 15 Bootstrap[34]: Time 32.673231 seconds, bootstrap likelihood -151642.401058, best rearrangement setting 11 Bootstrap[35]: Time 32.392760 seconds, bootstrap likelihood -153565.013264, best rearrangement setting 8 Bootstrap[36]: Time 32.937373 seconds, bootstrap likelihood -152391.540851, best rearrangement setting 9 Bootstrap[37]: Time 32.141823 seconds, bootstrap likelihood -153128.116264, best rearrangement setting 11 Bootstrap[38]: Time 29.245887 seconds, bootstrap likelihood -154518.130797, best rearrangement setting 8 Bootstrap[39]: Time 32.076082 seconds, bootstrap likelihood -153991.964795, best rearrangement setting 13 Bootstrap[40]: Time 31.021136 seconds, bootstrap likelihood -153918.513483, best rearrangement setting 13 Bootstrap[41]: Time 34.019018 seconds, bootstrap likelihood -153191.205877, best rearrangement setting 10 Bootstrap[42]: Time 28.667911 seconds, bootstrap likelihood -153806.304288, best rearrangement setting 5 Bootstrap[43]: Time 33.042667 seconds, bootstrap likelihood -155018.127673, best rearrangement setting 14 Bootstrap[44]: Time 31.448485 seconds, bootstrap likelihood -154599.065380, best rearrangement setting 10 Bootstrap[45]: Time 31.752728 seconds, bootstrap likelihood -153836.907944, best rearrangement setting 15 Bootstrap[46]: Time 32.604092 seconds, bootstrap likelihood -153394.903178, best rearrangement setting 14 Bootstrap[47]: Time 31.605226 seconds, bootstrap likelihood -153183.410157, best rearrangement setting 8 Bootstrap[48]: Time 32.658703 seconds, bootstrap likelihood -154404.254178, best rearrangement setting 6 Bootstrap[49]: Time 32.662018 seconds, bootstrap likelihood -154489.082482, best rearrangement setting 7 Bootstrap[50]: Time 10.205970 seconds, bootstrap likelihood -154197.191925, best rearrangement setting 7 Bootstrap[51]: Time 10.209953 seconds, bootstrap likelihood -153167.563921, best rearrangement setting 11 Bootstrap[52]: Time 28.839247 seconds, bootstrap likelihood -153003.606865, best rearrangement setting 12 Bootstrap[53]: Time 32.365167 seconds, bootstrap likelihood -155470.645264, best rearrangement setting 8 Bootstrap[54]: Time 9.281435 seconds, bootstrap likelihood -154156.696238, best rearrangement setting 9 Bootstrap[55]: Time 9.236416 seconds, bootstrap likelihood -153516.505901, best rearrangement setting 11 Bootstrap[56]: Time 28.071198 seconds, bootstrap likelihood -153595.811677, best rearrangement setting 5 Bootstrap[57]: Time 31.802818 seconds, bootstrap likelihood -154602.391278, best rearrangement setting 7 Bootstrap[58]: Time 10.323852 seconds, bootstrap likelihood -153167.235745, best rearrangement setting 10 Bootstrap[59]: Time 8.982326 seconds, bootstrap likelihood -154526.939835, best rearrangement setting 9 Bootstrap[60]: Time 9.353798 seconds, bootstrap likelihood -154008.589253, best rearrangement setting 7 Bootstrap[61]: Time 27.721454 seconds, bootstrap likelihood -151522.291785, best rearrangement setting 5 Bootstrap[62]: Time 34.956583 seconds, bootstrap likelihood -155386.286910, best rearrangement setting 11 Bootstrap[63]: Time 34.506761 seconds, bootstrap likelihood -153252.526367, best rearrangement setting 12 Bootstrap[64]: Time 9.594627 seconds, bootstrap likelihood -154760.306897, best rearrangement setting 7 Bootstrap[65]: Time 27.168749 seconds, bootstrap likelihood -153509.644498, best rearrangement setting 5 Bootstrap[66]: Time 27.715787 seconds, bootstrap likelihood -151601.590562, best rearrangement setting 5 Bootstrap[67]: Time 31.727281 seconds, bootstrap likelihood -154476.654699, best rearrangement setting 15 Bootstrap[68]: Time 31.876256 seconds, bootstrap likelihood -153616.204090, best rearrangement setting 11 Bootstrap[69]: Time 30.003716 seconds, bootstrap likelihood -152604.153555, best rearrangement setting 5 Bootstrap[70]: Time 32.879820 seconds, bootstrap likelihood -153971.501232, best rearrangement setting 8 Bootstrap[71]: Time 10.703620 seconds, bootstrap likelihood -154425.516176, best rearrangement setting 10 Bootstrap[72]: Time 33.431953 seconds, bootstrap likelihood -153845.511406, best rearrangement setting 11 Bootstrap[73]: Time 32.012990 seconds, bootstrap likelihood -153745.756335, best rearrangement setting 9 Bootstrap[74]: Time 30.053755 seconds, bootstrap likelihood -153308.942847, best rearrangement setting 5 Bootstrap[75]: Time 33.319600 seconds, bootstrap likelihood -154844.475190, best rearrangement setting 8 Bootstrap[76]: Time 31.198327 seconds, bootstrap likelihood -153075.931440, best rearrangement setting 9 Bootstrap[77]: Time 32.322409 seconds, bootstrap likelihood -153885.336426, best rearrangement setting 11 Bootstrap[78]: Time 9.221288 seconds, bootstrap likelihood -153794.977352, best rearrangement setting 15 Bootstrap[79]: Time 31.537151 seconds, bootstrap likelihood -153614.331631, best rearrangement setting 9 Bootstrap[80]: Time 11.057497 seconds, bootstrap likelihood -155658.374062, best rearrangement setting 15 Bootstrap[81]: Time 10.205454 seconds, bootstrap likelihood -152886.090030, best rearrangement setting 7 Bootstrap[82]: Time 10.281583 seconds, bootstrap likelihood -152847.974923, best rearrangement setting 6 Bootstrap[83]: Time 32.065662 seconds, bootstrap likelihood -153849.284513, best rearrangement setting 10 Bootstrap[84]: Time 31.318674 seconds, bootstrap likelihood -154804.573447, best rearrangement setting 11 Bootstrap[85]: Time 10.502363 seconds, bootstrap likelihood -152268.793978, best rearrangement setting 8 Bootstrap[86]: Time 10.680583 seconds, bootstrap likelihood -152533.192402, best rearrangement setting 7 Bootstrap[87]: Time 31.906215 seconds, bootstrap likelihood -152410.133199, best rearrangement setting 7 Bootstrap[88]: Time 31.880537 seconds, bootstrap likelihood -153259.739758, best rearrangement setting 12 Bootstrap[89]: Time 32.455552 seconds, bootstrap likelihood -152113.636890, best rearrangement setting 10 Bootstrap[90]: Time 9.512429 seconds, bootstrap likelihood -152567.320276, best rearrangement setting 8 Bootstrap[91]: Time 31.958202 seconds, bootstrap likelihood -152915.613297, best rearrangement setting 12 Bootstrap[92]: Time 33.257294 seconds, bootstrap likelihood -154788.177653, best rearrangement setting 13 Bootstrap[93]: Time 10.630490 seconds, bootstrap likelihood -152519.443923, best rearrangement setting 15 Bootstrap[94]: Time 11.069931 seconds, bootstrap likelihood -152919.695830, best rearrangement setting 5 Bootstrap[95]: Time 10.676221 seconds, bootstrap likelihood -153676.900785, best rearrangement setting 5 Bootstrap[96]: Time 10.485076 seconds, bootstrap likelihood -152678.111345, best rearrangement setting 13 Bootstrap[97]: Time 33.168151 seconds, bootstrap likelihood -153781.346481, best rearrangement setting 11 Bootstrap[98]: Time 32.547257 seconds, bootstrap likelihood -153232.051821, best rearrangement setting 6 Bootstrap[99]: Time 10.965321 seconds, bootstrap likelihood -153698.362393, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 2851.439765 seconds Average Time per Rapid Bootstrap 28.514398 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 1802.586471 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 90.093792 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.472075 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.537263 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.084021 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.90perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 1994.615465 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1801.926957 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 90.346393 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.490734 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.536232 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.083673 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.90perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -153724.354891 Slow ML Search 1 Likelihood: -153724.354890 Slow ML Search 2 Likelihood: -153724.354891 Slow ML Search 3 Likelihood: -153724.354890 Slow ML Search 4 Likelihood: -153724.354890 Slow ML Search 5 Likelihood: -153724.354890 Slow ML Search 6 Likelihood: -153724.354893 Slow ML Search 7 Likelihood: -153724.354893 Slow ML Search 8 Likelihood: -153724.354890 Slow ML Search 9 Likelihood: -153724.354891 Slow ML optimization finished Slow ML search Time: 1474.801344 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1801.866529 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 89.864846 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.457420 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.540050 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.90perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.085387 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.90perc_cov_Partition_No Name Provided Thorough ML search Time: 552.055550 seconds Final ML Optimization Likelihood: -153724.391416 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.692709 Tree-Length: 17.016368 rate A <-> R: 0.369219 rate A <-> N: 0.564205 rate A <-> D: 1.885186 rate A <-> C: 7.340533 rate A <-> Q: 0.171753 rate A <-> E: 2.340960 rate A <-> G: 6.405319 rate A <-> H: 0.387158 rate A <-> I: 1.877555 rate A <-> L: 1.456863 rate A <-> K: 0.149063 rate A <-> M: 1.947095 rate A <-> F: 0.982852 rate A <-> P: 4.139398 rate A <-> S: 23.004613 rate A <-> T: 14.631501 rate A <-> W: 0.171855 rate A <-> Y: 0.000000 rate A <-> V: 14.060403 rate R <-> N: 0.616219 rate R <-> D: 0.000000 rate R <-> C: 1.013657 rate R <-> Q: 5.286288 rate R <-> E: 0.689333 rate R <-> G: 1.102003 rate R <-> H: 4.227067 rate R <-> I: 0.295974 rate R <-> L: 0.400621 rate R <-> K: 21.795878 rate R <-> M: 1.169348 rate R <-> F: 0.105203 rate R <-> P: 0.309014 rate R <-> S: 1.259657 rate R <-> T: 0.715664 rate R <-> W: 1.082463 rate R <-> Y: 0.353183 rate R <-> V: 0.000000 rate N <-> D: 14.449674 rate N <-> C: 0.829691 rate N <-> Q: 7.273249 rate N <-> E: 3.524463 rate N <-> G: 2.483458 rate N <-> H: 8.644436 rate N <-> I: 2.439526 rate N <-> L: 0.947952 rate N <-> K: 8.387191 rate N <-> M: 0.769756 rate N <-> F: 0.568624 rate N <-> P: 0.469196 rate N <-> S: 14.993174 rate N <-> T: 9.029731 rate N <-> W: 0.258486 rate N <-> Y: 3.871196 rate N <-> V: 0.332411 rate D <-> C: 0.886882 rate D <-> Q: 0.000000 rate D <-> E: 30.361063 rate D <-> G: 2.111080 rate D <-> H: 2.147255 rate D <-> I: 0.107226 rate D <-> L: 0.077760 rate D <-> K: 0.846179 rate D <-> M: 0.000000 rate D <-> F: 0.081402 rate D <-> P: 0.934009 rate D <-> S: 3.426098 rate D <-> T: 1.107190 rate D <-> W: 0.210976 rate D <-> Y: 0.469041 rate D <-> V: 0.359781 rate C <-> Q: 0.213040 rate C <-> E: 0.079279 rate C <-> G: 2.347381 rate C <-> H: 3.483197 rate C <-> I: 1.331469 rate C <-> L: 1.492257 rate C <-> K: 0.000000 rate C <-> M: 2.465379 rate C <-> F: 1.802736 rate C <-> P: 0.000000 rate C <-> S: 10.338529 rate C <-> T: 3.706438 rate C <-> W: 1.593300 rate C <-> Y: 4.366959 rate C <-> V: 4.897276 rate Q <-> E: 7.636984 rate Q <-> G: 0.138786 rate Q <-> H: 20.297318 rate Q <-> I: 0.556477 rate Q <-> L: 1.540709 rate Q <-> K: 7.016887 rate Q <-> M: 1.582022 rate Q <-> F: 0.309491 rate Q <-> P: 3.482693 rate Q <-> S: 2.253049 rate Q <-> T: 3.253321 rate Q <-> W: 0.000000 rate Q <-> Y: 1.239246 rate Q <-> V: 0.000000 rate E <-> G: 1.896701 rate E <-> H: 0.273809 rate E <-> I: 0.351516 rate E <-> L: 0.368108 rate E <-> K: 3.782876 rate E <-> M: 0.167570 rate E <-> F: 0.147276 rate E <-> P: 0.359235 rate E <-> S: 2.377828 rate E <-> T: 1.751432 rate E <-> W: 0.153392 rate E <-> Y: 0.858050 rate E <-> V: 0.657250 rate G <-> H: 0.626903 rate G <-> I: 0.110188 rate G <-> L: 0.025626 rate G <-> K: 0.422220 rate G <-> M: 0.373933 rate G <-> F: 0.248850 rate G <-> P: 0.289757 rate G <-> S: 6.164169 rate G <-> T: 0.470862 rate G <-> W: 0.832994 rate G <-> Y: 0.000000 rate G <-> V: 0.623756 rate H <-> I: 0.142321 rate H <-> L: 0.872842 rate H <-> K: 0.382609 rate H <-> M: 0.000000 rate H <-> F: 0.618176 rate H <-> P: 0.461744 rate H <-> S: 1.881454 rate H <-> T: 1.241196 rate H <-> W: 0.000000 rate H <-> Y: 11.863039 rate H <-> V: 0.000000 rate I <-> L: 17.839179 rate I <-> K: 1.300440 rate I <-> M: 15.569378 rate I <-> F: 3.394335 rate I <-> P: 0.127398 rate I <-> S: 1.078264 rate I <-> T: 8.335562 rate I <-> W: 0.499320 rate I <-> Y: 2.230254 rate I <-> V: 49.074662 rate L <-> K: 0.523536 rate L <-> M: 13.516341 rate L <-> F: 6.229670 rate L <-> P: 1.025855 rate L <-> S: 1.766760 rate L <-> T: 1.623603 rate L <-> W: 1.375849 rate L <-> Y: 1.291026 rate L <-> V: 5.128585 rate K <-> M: 0.496831 rate K <-> F: 0.133037 rate K <-> P: 0.392277 rate K <-> S: 2.032054 rate K <-> T: 1.815735 rate K <-> W: 0.085585 rate K <-> Y: 0.746592 rate K <-> V: 0.238788 rate M <-> F: 1.614062 rate M <-> P: 0.292369 rate M <-> S: 0.666493 rate M <-> T: 5.080437 rate M <-> W: 0.410613 rate M <-> Y: 0.730951 rate M <-> V: 7.935789 rate F <-> P: 0.239596 rate F <-> S: 1.298235 rate F <-> T: 0.626912 rate F <-> W: 1.188581 rate F <-> Y: 10.707630 rate F <-> V: 1.407640 rate P <-> S: 6.018594 rate P <-> T: 3.237515 rate P <-> W: 0.346137 rate P <-> Y: 0.813196 rate P <-> V: 1.225107 rate S <-> T: 22.201174 rate S <-> W: 0.286086 rate S <-> Y: 1.615357 rate S <-> V: 1.433252 rate T <-> W: 0.099340 rate T <-> Y: 0.851639 rate T <-> V: 12.008022 rate W <-> Y: 2.821603 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 4021.563543 secs or 1.117101 hours Combined Bootstrap and ML search took 6873.004163 secs or 1.909168 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.90perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.90perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-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-PROTGAMMAGTR-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-PROTGAMMAGTR-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-PROTGAMMAGTR-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-PROTGAMMAGTR-supermatrix.mito.full-assemblies.90perc_cov Overall execution time for full ML analysis: 6873.074151 secs or 1.909187 hours or 0.079549 days