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 10039 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 20.52% 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: 10039 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.50perc_cov.fa -n RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.50perc_cov -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 2114.103778 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 127.733140 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 10.441806 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.283646 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.50perc_cov_Partition_No Name Provided Time for BS model parameter optimization 393.303554 Bootstrap[0]: Time 435.719218 seconds, bootstrap likelihood -181269.409178, best rearrangement setting 13 Bootstrap[1]: Time 40.510487 seconds, bootstrap likelihood -181596.954726, best rearrangement setting 13 Bootstrap[2]: Time 41.887685 seconds, bootstrap likelihood -183116.175723, best rearrangement setting 12 Bootstrap[3]: Time 39.889038 seconds, bootstrap likelihood -183342.119390, best rearrangement setting 15 Bootstrap[4]: Time 40.831766 seconds, bootstrap likelihood -182866.304090, best rearrangement setting 10 Bootstrap[5]: Time 39.693443 seconds, bootstrap likelihood -184417.683089, best rearrangement setting 10 Bootstrap[6]: Time 38.888021 seconds, bootstrap likelihood -182961.721646, best rearrangement setting 6 Bootstrap[7]: Time 39.324140 seconds, bootstrap likelihood -183450.531551, best rearrangement setting 14 Bootstrap[8]: Time 37.535282 seconds, bootstrap likelihood -181955.890876, best rearrangement setting 5 Bootstrap[9]: Time 38.028859 seconds, bootstrap likelihood -183554.730999, best rearrangement setting 7 Bootstrap[10]: Time 38.793320 seconds, bootstrap likelihood -182602.646043, best rearrangement setting 7 Bootstrap[11]: Time 36.558554 seconds, bootstrap likelihood -181918.545589, best rearrangement setting 5 Bootstrap[12]: Time 41.082978 seconds, bootstrap likelihood -183010.899099, best rearrangement setting 8 Bootstrap[13]: Time 38.877284 seconds, bootstrap likelihood -182940.594859, best rearrangement setting 7 Bootstrap[14]: Time 40.278308 seconds, bootstrap likelihood -184564.301276, best rearrangement setting 12 Bootstrap[15]: Time 39.518441 seconds, bootstrap likelihood -181780.341686, best rearrangement setting 15 Bootstrap[16]: Time 42.253157 seconds, bootstrap likelihood -183321.621331, best rearrangement setting 12 Bootstrap[17]: Time 40.396518 seconds, bootstrap likelihood -183510.298559, best rearrangement setting 12 Bootstrap[18]: Time 38.743676 seconds, bootstrap likelihood -181544.661490, best rearrangement setting 5 Bootstrap[19]: Time 41.090880 seconds, bootstrap likelihood -181621.037410, best rearrangement setting 8 Bootstrap[20]: Time 42.141735 seconds, bootstrap likelihood -181813.049311, best rearrangement setting 10 Bootstrap[21]: Time 37.965684 seconds, bootstrap likelihood -182819.963658, best rearrangement setting 6 Bootstrap[22]: Time 38.190577 seconds, bootstrap likelihood -182817.952335, best rearrangement setting 5 Bootstrap[23]: Time 40.972251 seconds, bootstrap likelihood -185054.836952, best rearrangement setting 7 Bootstrap[24]: Time 38.579352 seconds, bootstrap likelihood -180775.309612, best rearrangement setting 8 Bootstrap[25]: Time 38.282110 seconds, bootstrap likelihood -181490.848795, best rearrangement setting 6 Bootstrap[26]: Time 41.967663 seconds, bootstrap likelihood -182762.055028, best rearrangement setting 12 Bootstrap[27]: Time 41.361870 seconds, bootstrap likelihood -182154.249664, best rearrangement setting 10 Bootstrap[28]: Time 41.977260 seconds, bootstrap likelihood -180911.246739, best rearrangement setting 11 Bootstrap[29]: Time 39.593796 seconds, bootstrap likelihood -183336.534892, best rearrangement setting 12 Bootstrap[30]: Time 12.993185 seconds, bootstrap likelihood -184236.677865, best rearrangement setting 15 Bootstrap[31]: Time 38.215039 seconds, bootstrap likelihood -183249.935979, best rearrangement setting 15 Bootstrap[32]: Time 12.979300 seconds, bootstrap likelihood -182746.379980, best rearrangement setting 6 Bootstrap[33]: Time 11.877639 seconds, bootstrap likelihood -182723.150570, best rearrangement setting 15 Bootstrap[34]: Time 39.525188 seconds, bootstrap likelihood -182047.816791, best rearrangement setting 11 Bootstrap[35]: Time 41.876833 seconds, bootstrap likelihood -183114.946732, best rearrangement setting 8 Bootstrap[36]: Time 39.756222 seconds, bootstrap likelihood -181074.358939, best rearrangement setting 9 Bootstrap[37]: Time 41.152838 seconds, bootstrap likelihood -181386.756013, best rearrangement setting 11 Bootstrap[38]: Time 40.304424 seconds, bootstrap likelihood -183345.027372, best rearrangement setting 8 Bootstrap[39]: Time 41.945472 seconds, bootstrap likelihood -184157.006189, best rearrangement setting 13 Bootstrap[40]: Time 42.448461 seconds, bootstrap likelihood -181507.186971, best rearrangement setting 13 Bootstrap[41]: Time 40.612075 seconds, bootstrap likelihood -182462.710970, best rearrangement setting 10 Bootstrap[42]: Time 38.351661 seconds, bootstrap likelihood -184406.534715, best rearrangement setting 5 Bootstrap[43]: Time 40.158810 seconds, bootstrap likelihood -182684.360446, best rearrangement setting 14 Bootstrap[44]: Time 41.475649 seconds, bootstrap likelihood -182672.342139, best rearrangement setting 10 Bootstrap[45]: Time 41.719396 seconds, bootstrap likelihood -181713.028430, best rearrangement setting 15 Bootstrap[46]: Time 44.264609 seconds, bootstrap likelihood -183417.496638, best rearrangement setting 14 Bootstrap[47]: Time 40.466871 seconds, bootstrap likelihood -182597.748498, best rearrangement setting 8 Bootstrap[48]: Time 38.537078 seconds, bootstrap likelihood -181509.749162, best rearrangement setting 6 Bootstrap[49]: Time 38.820224 seconds, bootstrap likelihood -182399.163571, best rearrangement setting 7 Bootstrap[50]: Time 36.687590 seconds, bootstrap likelihood -180920.921641, best rearrangement setting 7 Bootstrap[51]: Time 41.032912 seconds, bootstrap likelihood -183559.452558, best rearrangement setting 11 Bootstrap[52]: Time 38.259518 seconds, bootstrap likelihood -182696.372591, best rearrangement setting 12 Bootstrap[53]: Time 39.446683 seconds, bootstrap likelihood -181182.829879, best rearrangement setting 8 Bootstrap[54]: Time 40.713531 seconds, bootstrap likelihood -183338.393586, best rearrangement setting 9 Bootstrap[55]: Time 40.452654 seconds, bootstrap likelihood -183461.360180, best rearrangement setting 11 Bootstrap[56]: Time 35.858529 seconds, bootstrap likelihood -183871.784115, best rearrangement setting 5 Bootstrap[57]: Time 38.229281 seconds, bootstrap likelihood -184111.922149, best rearrangement setting 7 Bootstrap[58]: Time 39.968656 seconds, bootstrap likelihood -183597.274835, best rearrangement setting 10 Bootstrap[59]: Time 39.237331 seconds, bootstrap likelihood -182945.362883, best rearrangement setting 9 Bootstrap[60]: Time 39.031199 seconds, bootstrap likelihood -181688.346784, best rearrangement setting 7 Bootstrap[61]: Time 35.426250 seconds, bootstrap likelihood -182890.685825, best rearrangement setting 5 Bootstrap[62]: Time 39.294954 seconds, bootstrap likelihood -182100.267212, best rearrangement setting 11 Bootstrap[63]: Time 40.819025 seconds, bootstrap likelihood -184419.280980, best rearrangement setting 12 Bootstrap[64]: Time 38.810484 seconds, bootstrap likelihood -182111.474188, best rearrangement setting 7 Bootstrap[65]: Time 37.327549 seconds, bootstrap likelihood -181061.844462, best rearrangement setting 5 Bootstrap[66]: Time 13.340977 seconds, bootstrap likelihood -182182.387169, best rearrangement setting 5 Bootstrap[67]: Time 12.240911 seconds, bootstrap likelihood -181979.583964, best rearrangement setting 15 Bootstrap[68]: Time 39.051563 seconds, bootstrap likelihood -183389.692576, best rearrangement setting 11 Bootstrap[69]: Time 37.814929 seconds, bootstrap likelihood -182975.220934, best rearrangement setting 5 Bootstrap[70]: Time 40.398273 seconds, bootstrap likelihood -184565.974515, best rearrangement setting 8 Bootstrap[71]: Time 39.163135 seconds, bootstrap likelihood -182345.805731, best rearrangement setting 10 Bootstrap[72]: Time 41.468863 seconds, bootstrap likelihood -182770.657215, best rearrangement setting 11 Bootstrap[73]: Time 41.170027 seconds, bootstrap likelihood -181424.460464, best rearrangement setting 9 Bootstrap[74]: Time 36.755912 seconds, bootstrap likelihood -180766.816188, best rearrangement setting 5 Bootstrap[75]: Time 40.175489 seconds, bootstrap likelihood -182762.358094, best rearrangement setting 8 Bootstrap[76]: Time 42.930975 seconds, bootstrap likelihood -181891.720668, best rearrangement setting 9 Bootstrap[77]: Time 40.311457 seconds, bootstrap likelihood -182031.826867, best rearrangement setting 11 Bootstrap[78]: Time 38.901735 seconds, bootstrap likelihood -183095.561605, best rearrangement setting 15 Bootstrap[79]: Time 39.336830 seconds, bootstrap likelihood -182519.365023, best rearrangement setting 9 Bootstrap[80]: Time 41.513440 seconds, bootstrap likelihood -183764.535727, best rearrangement setting 15 Bootstrap[81]: Time 37.818303 seconds, bootstrap likelihood -182060.596945, best rearrangement setting 7 Bootstrap[82]: Time 37.450590 seconds, bootstrap likelihood -180971.022693, best rearrangement setting 6 Bootstrap[83]: Time 40.260428 seconds, bootstrap likelihood -182566.207259, best rearrangement setting 10 Bootstrap[84]: Time 40.871120 seconds, bootstrap likelihood -180953.847578, best rearrangement setting 11 Bootstrap[85]: Time 41.547590 seconds, bootstrap likelihood -183472.614247, best rearrangement setting 8 Bootstrap[86]: Time 41.427321 seconds, bootstrap likelihood -181346.560873, best rearrangement setting 7 Bootstrap[87]: Time 41.428384 seconds, bootstrap likelihood -182940.757045, best rearrangement setting 7 Bootstrap[88]: Time 39.587361 seconds, bootstrap likelihood -183510.516820, best rearrangement setting 12 Bootstrap[89]: Time 42.632780 seconds, bootstrap likelihood -181246.922118, best rearrangement setting 10 Bootstrap[90]: Time 42.866036 seconds, bootstrap likelihood -182507.206899, best rearrangement setting 8 Bootstrap[91]: Time 40.303890 seconds, bootstrap likelihood -180384.709021, best rearrangement setting 12 Bootstrap[92]: Time 40.753995 seconds, bootstrap likelihood -182516.019606, best rearrangement setting 13 Bootstrap[93]: Time 42.847145 seconds, bootstrap likelihood -183278.266547, best rearrangement setting 15 Bootstrap[94]: Time 37.666130 seconds, bootstrap likelihood -181678.664210, best rearrangement setting 5 Bootstrap[95]: Time 38.751140 seconds, bootstrap likelihood -184332.332169, best rearrangement setting 5 Bootstrap[96]: Time 41.447204 seconds, bootstrap likelihood -183167.210950, best rearrangement setting 13 Bootstrap[97]: Time 40.250485 seconds, bootstrap likelihood -181880.268335, best rearrangement setting 11 Bootstrap[98]: Time 41.123265 seconds, bootstrap likelihood -182736.112704, best rearrangement setting 6 Bootstrap[99]: Time 42.409935 seconds, bootstrap likelihood -181262.086452, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 4255.436576 seconds Average Time per Rapid Bootstrap 42.554366 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 2115.641835 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 128.158185 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 10.498243 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.290880 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.204395 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.043554 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.50perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 3326.778109 seconds Printed linked AA GTR matrix that achieved an overall improvement of 2114.433217 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 127.942165 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 10.466486 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.288711 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.204535 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.043687 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.50perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -182806.128689 Slow ML Search 1 Likelihood: -182806.128688 Slow ML Search 2 Likelihood: -182806.128688 Slow ML Search 3 Likelihood: -182806.128689 Slow ML Search 4 Likelihood: -182806.128689 Slow ML Search 5 Likelihood: -182806.128690 Slow ML Search 6 Likelihood: -182806.128688 Slow ML Search 7 Likelihood: -182806.128689 Slow ML Search 8 Likelihood: -182806.128689 Slow ML Search 9 Likelihood: -182806.128690 Slow ML optimization finished Slow ML search Time: 1917.736136 seconds Printed linked AA GTR matrix that achieved an overall improvement of 2114.725762 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 128.065955 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 10.486586 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.288480 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.203912 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.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.043477 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.50perc_cov_Partition_No Name Provided Thorough ML search Time: 753.441103 seconds Final ML Optimization Likelihood: -182806.121469 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.632228 Tree-Length: 21.854032 rate A <-> R: 0.446754 rate A <-> N: 0.502864 rate A <-> D: 2.662895 rate A <-> C: 6.834319 rate A <-> Q: 0.536153 rate A <-> E: 3.434723 rate A <-> G: 7.999084 rate A <-> H: 0.438672 rate A <-> I: 1.958572 rate A <-> L: 1.595242 rate A <-> K: 0.268286 rate A <-> M: 1.812572 rate A <-> F: 0.882074 rate A <-> P: 5.076774 rate A <-> S: 21.989562 rate A <-> T: 15.862155 rate A <-> W: 0.108634 rate A <-> Y: 0.022858 rate A <-> V: 14.404703 rate R <-> N: 0.484709 rate R <-> D: 0.179087 rate R <-> C: 1.817599 rate R <-> Q: 6.044242 rate R <-> E: 0.899673 rate R <-> G: 1.821448 rate R <-> H: 4.961153 rate R <-> I: 0.300734 rate R <-> L: 0.445135 rate R <-> K: 21.205784 rate R <-> M: 1.315893 rate R <-> F: 0.105378 rate R <-> P: 0.956030 rate R <-> S: 1.334135 rate R <-> T: 0.825759 rate R <-> W: 1.249799 rate R <-> Y: 0.424562 rate R <-> V: 0.215308 rate N <-> D: 14.433651 rate N <-> C: 0.910811 rate N <-> Q: 6.654908 rate N <-> E: 2.859757 rate N <-> G: 2.338957 rate N <-> H: 8.736523 rate N <-> I: 2.710566 rate N <-> L: 0.819544 rate N <-> K: 8.302424 rate N <-> M: 0.621635 rate N <-> F: 0.599798 rate N <-> P: 0.340819 rate N <-> S: 14.912746 rate N <-> T: 8.529310 rate N <-> W: 0.163998 rate N <-> Y: 3.481014 rate N <-> V: 0.411892 rate D <-> C: 0.828690 rate D <-> Q: 0.035276 rate D <-> E: 32.655963 rate D <-> G: 3.399886 rate D <-> H: 1.585961 rate D <-> I: 0.215335 rate D <-> L: 0.174584 rate D <-> K: 1.016552 rate D <-> M: 0.193239 rate D <-> F: 0.117589 rate D <-> P: 1.366529 rate D <-> S: 3.346677 rate D <-> T: 2.064182 rate D <-> W: 0.165840 rate D <-> Y: 0.648927 rate D <-> V: 0.408316 rate C <-> Q: 0.156723 rate C <-> E: 0.000000 rate C <-> G: 2.904120 rate C <-> H: 3.371850 rate C <-> I: 1.213441 rate C <-> L: 1.352124 rate C <-> K: 0.000000 rate C <-> M: 2.033024 rate C <-> F: 1.835885 rate C <-> P: 0.138249 rate C <-> S: 9.588670 rate C <-> T: 3.589887 rate C <-> W: 1.456504 rate C <-> Y: 5.257421 rate C <-> V: 4.627294 rate Q <-> E: 8.530836 rate Q <-> G: 0.044123 rate Q <-> H: 24.563954 rate Q <-> I: 0.571197 rate Q <-> L: 1.799843 rate Q <-> K: 7.408414 rate Q <-> M: 1.923751 rate Q <-> F: 0.336605 rate Q <-> P: 4.576882 rate Q <-> S: 2.669571 rate Q <-> T: 2.934003 rate Q <-> W: 0.000000 rate Q <-> Y: 1.741535 rate Q <-> V: 0.149910 rate E <-> G: 3.636669 rate E <-> H: 1.509835 rate E <-> I: 0.255137 rate E <-> L: 0.331741 rate E <-> K: 4.047499 rate E <-> M: 0.064613 rate E <-> F: 0.109932 rate E <-> P: 1.097377 rate E <-> S: 2.211272 rate E <-> T: 1.879881 rate E <-> W: 0.134789 rate E <-> Y: 0.717054 rate E <-> V: 1.121448 rate G <-> H: 0.597198 rate G <-> I: 0.123312 rate G <-> L: 0.053361 rate G <-> K: 0.417864 rate G <-> M: 0.388742 rate G <-> F: 0.237530 rate G <-> P: 0.251147 rate G <-> S: 6.594932 rate G <-> T: 0.579215 rate G <-> W: 1.144225 rate G <-> Y: 0.000000 rate G <-> V: 0.887513 rate H <-> I: 0.086530 rate H <-> L: 1.101565 rate H <-> K: 0.584248 rate H <-> M: 0.000000 rate H <-> F: 0.509434 rate H <-> P: 1.474692 rate H <-> S: 1.907493 rate H <-> T: 1.646010 rate H <-> W: 0.642533 rate H <-> Y: 14.017482 rate H <-> V: 0.000000 rate I <-> L: 16.980583 rate I <-> K: 1.501287 rate I <-> M: 16.203755 rate I <-> F: 3.360800 rate I <-> P: 0.068004 rate I <-> S: 1.045730 rate I <-> T: 8.638037 rate I <-> W: 0.451056 rate I <-> Y: 2.341715 rate I <-> V: 48.184843 rate L <-> K: 0.587663 rate L <-> M: 13.510873 rate L <-> F: 5.943529 rate L <-> P: 1.474339 rate L <-> S: 1.846974 rate L <-> T: 1.865298 rate L <-> W: 1.453278 rate L <-> Y: 1.282570 rate L <-> V: 4.633527 rate K <-> M: 0.517800 rate K <-> F: 0.137890 rate K <-> P: 0.552529 rate K <-> S: 1.913157 rate K <-> T: 1.867539 rate K <-> W: 0.093322 rate K <-> Y: 0.764735 rate K <-> V: 0.281662 rate M <-> F: 1.441753 rate M <-> P: 0.135597 rate M <-> S: 0.685961 rate M <-> T: 5.048192 rate M <-> W: 0.403926 rate M <-> Y: 0.923211 rate M <-> V: 8.786155 rate F <-> P: 0.319234 rate F <-> S: 1.354493 rate F <-> T: 0.696655 rate F <-> W: 1.244216 rate F <-> Y: 10.029067 rate F <-> V: 1.345546 rate P <-> S: 6.864540 rate P <-> T: 3.932340 rate P <-> W: 0.291179 rate P <-> Y: 0.922494 rate P <-> V: 1.673542 rate S <-> T: 22.011260 rate S <-> W: 0.380737 rate S <-> Y: 1.651236 rate S <-> V: 1.569628 rate T <-> W: 0.261916 rate T <-> Y: 0.804334 rate T <-> V: 11.789531 rate W <-> Y: 2.702355 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.043096 freq pi(R): 0.037294 freq pi(N): 0.064440 freq pi(D): 0.029512 freq pi(C): 0.012359 freq pi(Q): 0.017568 freq pi(E): 0.036269 freq pi(G): 0.039740 freq pi(H): 0.016776 freq pi(I): 0.074320 freq pi(L): 0.123921 freq pi(K): 0.080877 freq pi(M): 0.017251 freq pi(F): 0.141601 freq pi(P): 0.021928 freq pi(S): 0.074703 freq pi(T): 0.044918 freq pi(W): 0.015363 freq pi(Y): 0.053555 freq pi(V): 0.054508 ML search took 5998.055952 secs or 1.666127 hours Combined Bootstrap and ML search took 10253.493441 secs or 2.848193 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.50perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.50perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.50perc_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.50perc_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.50perc_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.50perc_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.50perc_cov Overall execution time for full ML analysis: 10253.590340 secs or 2.848220 hours or 0.118676 days