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 350 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 70.67% 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: 350 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Scrippsiella-hangoei_like-SHHI_4.MUSCLE.fa -n Scrippsiella-hangoei_like-SHHI_4.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.074348 Bootstrap[0]: Time 2.716463 seconds, bootstrap likelihood -7716.897236, best rearrangement setting 13 Bootstrap[1]: Time 2.455920 seconds, bootstrap likelihood -6861.943257, best rearrangement setting 13 Bootstrap[2]: Time 1.961188 seconds, bootstrap likelihood -7462.532465, best rearrangement setting 12 Bootstrap[3]: Time 1.976401 seconds, bootstrap likelihood -6897.277937, best rearrangement setting 15 Bootstrap[4]: Time 1.820344 seconds, bootstrap likelihood -7189.199033, best rearrangement setting 10 Bootstrap[5]: Time 2.439819 seconds, bootstrap likelihood -7263.301018, best rearrangement setting 10 Bootstrap[6]: Time 2.838836 seconds, bootstrap likelihood -6692.710631, best rearrangement setting 6 Bootstrap[7]: Time 2.312086 seconds, bootstrap likelihood -7473.162651, best rearrangement setting 14 Bootstrap[8]: Time 2.425865 seconds, bootstrap likelihood -6706.286565, best rearrangement setting 5 Bootstrap[9]: Time 2.275410 seconds, bootstrap likelihood -6845.617609, best rearrangement setting 7 Bootstrap[10]: Time 2.194373 seconds, bootstrap likelihood -7424.913833, best rearrangement setting 7 Bootstrap[11]: Time 2.208058 seconds, bootstrap likelihood -7573.707277, best rearrangement setting 5 Bootstrap[12]: Time 1.908628 seconds, bootstrap likelihood -7078.744993, best rearrangement setting 8 Bootstrap[13]: Time 2.475251 seconds, bootstrap likelihood -7006.585741, best rearrangement setting 7 Bootstrap[14]: Time 2.196143 seconds, bootstrap likelihood -7607.852267, best rearrangement setting 12 Bootstrap[15]: Time 2.600011 seconds, bootstrap likelihood -6881.628859, best rearrangement setting 15 Bootstrap[16]: Time 2.042961 seconds, bootstrap likelihood -7383.792217, best rearrangement setting 12 Bootstrap[17]: Time 1.924621 seconds, bootstrap likelihood -7119.669472, best rearrangement setting 12 Bootstrap[18]: Time 2.644710 seconds, bootstrap likelihood -6799.442109, best rearrangement setting 5 Bootstrap[19]: Time 2.678142 seconds, bootstrap likelihood -7324.774735, best rearrangement setting 8 Bootstrap[20]: Time 2.495678 seconds, bootstrap likelihood -6366.306996, best rearrangement setting 10 Bootstrap[21]: Time 2.309983 seconds, bootstrap likelihood -7320.780622, best rearrangement setting 6 Bootstrap[22]: Time 2.343930 seconds, bootstrap likelihood -6914.408203, best rearrangement setting 5 Bootstrap[23]: Time 2.577791 seconds, bootstrap likelihood -7313.826055, best rearrangement setting 7 Bootstrap[24]: Time 2.689299 seconds, bootstrap likelihood -6757.109237, best rearrangement setting 8 Bootstrap[25]: Time 2.530061 seconds, bootstrap likelihood -7561.863887, best rearrangement setting 6 Bootstrap[26]: Time 2.430592 seconds, bootstrap likelihood -7180.954482, best rearrangement setting 12 Bootstrap[27]: Time 2.515414 seconds, bootstrap likelihood -6726.723945, best rearrangement setting 10 Bootstrap[28]: Time 2.293275 seconds, bootstrap likelihood -6570.657438, best rearrangement setting 11 Bootstrap[29]: Time 2.096126 seconds, bootstrap likelihood -6983.191697, best rearrangement setting 12 Bootstrap[30]: Time 1.909801 seconds, bootstrap likelihood -7383.433738, best rearrangement setting 15 Bootstrap[31]: Time 2.484531 seconds, bootstrap likelihood -6716.980693, best rearrangement setting 15 Bootstrap[32]: Time 2.092153 seconds, bootstrap likelihood -6642.447738, best rearrangement setting 6 Bootstrap[33]: Time 2.656074 seconds, bootstrap likelihood -7331.895306, best rearrangement setting 15 Bootstrap[34]: Time 2.520117 seconds, bootstrap likelihood -7287.537406, best rearrangement setting 11 Bootstrap[35]: Time 2.884780 seconds, bootstrap likelihood -6906.489327, best rearrangement setting 8 Bootstrap[36]: Time 2.160292 seconds, bootstrap likelihood -6859.810272, best rearrangement setting 9 Bootstrap[37]: Time 2.627315 seconds, bootstrap likelihood -6896.993760, best rearrangement setting 11 Bootstrap[38]: Time 2.553926 seconds, bootstrap likelihood -6853.918598, best rearrangement setting 8 Bootstrap[39]: Time 3.089810 seconds, bootstrap likelihood -7433.546642, best rearrangement setting 13 Bootstrap[40]: Time 2.868600 seconds, bootstrap likelihood -6722.737145, best rearrangement setting 13 Bootstrap[41]: Time 2.241419 seconds, bootstrap likelihood -7146.816645, best rearrangement setting 10 Bootstrap[42]: Time 2.418082 seconds, bootstrap likelihood -6947.569301, best rearrangement setting 5 Bootstrap[43]: Time 2.428243 seconds, bootstrap likelihood -6116.184846, best rearrangement setting 14 Bootstrap[44]: Time 2.097128 seconds, bootstrap likelihood -7247.789103, best rearrangement setting 10 Bootstrap[45]: Time 2.337962 seconds, bootstrap likelihood -7340.636968, best rearrangement setting 15 Bootstrap[46]: Time 2.643898 seconds, bootstrap likelihood -7290.852801, best rearrangement setting 14 Bootstrap[47]: Time 2.536681 seconds, bootstrap likelihood -7476.311084, best rearrangement setting 8 Bootstrap[48]: Time 2.258732 seconds, bootstrap likelihood -7463.380665, best rearrangement setting 6 Bootstrap[49]: Time 2.008028 seconds, bootstrap likelihood -7719.974763, best rearrangement setting 7 Bootstrap[50]: Time 2.185579 seconds, bootstrap likelihood -7570.912194, best rearrangement setting 7 Bootstrap[51]: Time 2.599145 seconds, bootstrap likelihood -7296.281677, best rearrangement setting 11 Bootstrap[52]: Time 2.384279 seconds, bootstrap likelihood -7149.230204, best rearrangement setting 12 Bootstrap[53]: Time 2.533170 seconds, bootstrap likelihood -7611.016869, best rearrangement setting 8 Bootstrap[54]: Time 2.615667 seconds, bootstrap likelihood -6951.774154, best rearrangement setting 9 Bootstrap[55]: Time 2.968162 seconds, bootstrap likelihood -6651.710977, best rearrangement setting 11 Bootstrap[56]: Time 2.245868 seconds, bootstrap likelihood -7547.673284, best rearrangement setting 5 Bootstrap[57]: Time 2.331253 seconds, bootstrap likelihood -6716.648162, best rearrangement setting 7 Bootstrap[58]: Time 2.517963 seconds, bootstrap likelihood -7634.186379, best rearrangement setting 10 Bootstrap[59]: Time 2.767605 seconds, bootstrap likelihood -6688.826256, best rearrangement setting 9 Bootstrap[60]: Time 2.196087 seconds, bootstrap likelihood -7372.192950, best rearrangement setting 7 Bootstrap[61]: Time 2.023092 seconds, bootstrap likelihood -6585.683464, best rearrangement setting 5 Bootstrap[62]: Time 2.210795 seconds, bootstrap likelihood -7159.968111, best rearrangement setting 11 Bootstrap[63]: Time 2.475697 seconds, bootstrap likelihood -7225.757041, best rearrangement setting 12 Bootstrap[64]: Time 2.131265 seconds, bootstrap likelihood -7299.701294, best rearrangement setting 7 Bootstrap[65]: Time 2.336726 seconds, bootstrap likelihood -7500.634537, best rearrangement setting 5 Bootstrap[66]: Time 2.488852 seconds, bootstrap likelihood -7015.283094, best rearrangement setting 5 Bootstrap[67]: Time 2.039781 seconds, bootstrap likelihood -6703.096694, best rearrangement setting 15 Bootstrap[68]: Time 2.375061 seconds, bootstrap likelihood -7351.171268, best rearrangement setting 11 Bootstrap[69]: Time 2.182176 seconds, bootstrap likelihood -7146.738417, best rearrangement setting 5 Bootstrap[70]: Time 2.357326 seconds, bootstrap likelihood -7137.732478, best rearrangement setting 8 Bootstrap[71]: Time 2.527715 seconds, bootstrap likelihood -6440.041258, best rearrangement setting 10 Bootstrap[72]: Time 2.585291 seconds, bootstrap likelihood -7262.702896, best rearrangement setting 11 Bootstrap[73]: Time 2.452793 seconds, bootstrap likelihood -7148.276350, best rearrangement setting 9 Bootstrap[74]: Time 2.241397 seconds, bootstrap likelihood -7082.464553, best rearrangement setting 5 Bootstrap[75]: Time 2.406161 seconds, bootstrap likelihood -7239.793153, best rearrangement setting 8 Bootstrap[76]: Time 2.515196 seconds, bootstrap likelihood -7122.760856, best rearrangement setting 9 Bootstrap[77]: Time 2.852129 seconds, bootstrap likelihood -7351.969544, best rearrangement setting 11 Bootstrap[78]: Time 2.799314 seconds, bootstrap likelihood -7043.843629, best rearrangement setting 15 Bootstrap[79]: Time 2.332325 seconds, bootstrap likelihood -7218.523922, best rearrangement setting 9 Bootstrap[80]: Time 2.670478 seconds, bootstrap likelihood -7576.747529, best rearrangement setting 15 Bootstrap[81]: Time 2.552868 seconds, bootstrap likelihood -6929.662240, best rearrangement setting 7 Bootstrap[82]: Time 2.528163 seconds, bootstrap likelihood -7310.087976, best rearrangement setting 6 Bootstrap[83]: Time 2.471434 seconds, bootstrap likelihood -6624.603606, best rearrangement setting 10 Bootstrap[84]: Time 2.285978 seconds, bootstrap likelihood -7165.933505, best rearrangement setting 11 Bootstrap[85]: Time 2.637046 seconds, bootstrap likelihood -6661.658911, best rearrangement setting 8 Bootstrap[86]: Time 2.493482 seconds, bootstrap likelihood -7684.508093, best rearrangement setting 7 Bootstrap[87]: Time 2.477336 seconds, bootstrap likelihood -7344.790507, best rearrangement setting 7 Bootstrap[88]: Time 2.628289 seconds, bootstrap likelihood -6224.454327, best rearrangement setting 12 Bootstrap[89]: Time 2.721151 seconds, bootstrap likelihood -7001.722242, best rearrangement setting 10 Bootstrap[90]: Time 2.657534 seconds, bootstrap likelihood -7582.089846, best rearrangement setting 8 Bootstrap[91]: Time 2.123873 seconds, bootstrap likelihood -6757.636539, best rearrangement setting 12 Bootstrap[92]: Time 1.978283 seconds, bootstrap likelihood -6884.922870, best rearrangement setting 13 Bootstrap[93]: Time 2.646478 seconds, bootstrap likelihood -6712.260741, best rearrangement setting 15 Bootstrap[94]: Time 2.179850 seconds, bootstrap likelihood -6874.701495, best rearrangement setting 5 Bootstrap[95]: Time 2.656147 seconds, bootstrap likelihood -7233.354486, best rearrangement setting 5 Bootstrap[96]: Time 2.219046 seconds, bootstrap likelihood -6546.824394, best rearrangement setting 13 Bootstrap[97]: Time 2.700161 seconds, bootstrap likelihood -6380.082772, best rearrangement setting 11 Bootstrap[98]: Time 2.163474 seconds, bootstrap likelihood -6827.458275, best rearrangement setting 6 Bootstrap[99]: Time 2.576808 seconds, bootstrap likelihood -7102.960192, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 241.326972 seconds Average Time per Rapid Bootstrap 2.413270 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 290.453071 seconds Slow ML Search 0 Likelihood: -7090.140825 Slow ML Search 1 Likelihood: -7090.140825 Slow ML Search 2 Likelihood: -7090.140825 Slow ML Search 3 Likelihood: -7090.140825 Slow ML Search 4 Likelihood: -7090.140825 Slow ML Search 5 Likelihood: -7090.140875 Slow ML Search 6 Likelihood: -7090.140875 Slow ML Search 7 Likelihood: -7090.140875 Slow ML Search 8 Likelihood: -7090.140885 Slow ML Search 9 Likelihood: -7090.140885 Slow ML optimization finished Slow ML search Time: 71.665884 seconds Thorough ML search Time: 10.073714 seconds Final ML Optimization Likelihood: -7090.140989 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.373135 Tree-Length: 28.333895 rate A <-> R: 0.399182 rate A <-> N: 0.259945 rate A <-> D: 0.371058 rate A <-> C: 2.337364 rate A <-> Q: 0.910775 rate A <-> E: 0.975241 rate A <-> G: 1.940106 rate A <-> H: 0.336984 rate A <-> I: 0.140697 rate A <-> L: 0.371240 rate A <-> K: 0.503815 rate A <-> M: 1.055520 rate A <-> F: 0.238237 rate A <-> P: 1.105868 rate A <-> S: 4.439041 rate A <-> T: 2.009090 rate A <-> W: 0.169702 rate A <-> Y: 0.205613 rate A <-> V: 2.392567 rate R <-> N: 0.706048 rate R <-> D: 0.116398 rate R <-> C: 0.501968 rate R <-> Q: 2.636754 rate R <-> E: 0.341785 rate R <-> G: 0.366408 rate R <-> H: 2.278690 rate R <-> I: 0.119250 rate R <-> L: 0.283449 rate R <-> K: 5.940467 rate R <-> M: 0.454623 rate R <-> F: 0.049508 rate R <-> P: 0.312264 rate R <-> S: 0.805843 rate R <-> T: 0.543695 rate R <-> W: 0.557424 rate R <-> Y: 0.295274 rate R <-> V: 0.160471 rate N <-> D: 4.766737 rate N <-> C: 0.496537 rate N <-> Q: 1.592389 rate N <-> E: 0.508692 rate N <-> G: 1.350015 rate N <-> H: 4.234381 rate N <-> I: 0.179830 rate N <-> L: 0.064256 rate N <-> K: 2.014327 rate N <-> M: 0.348390 rate N <-> F: 0.084068 rate N <-> P: 0.151925 rate N <-> S: 3.764032 rate N <-> T: 1.878729 rate N <-> W: 0.042610 rate N <-> Y: 0.574720 rate N <-> V: 0.078587 rate D <-> C: 0.058743 rate D <-> Q: 0.491483 rate D <-> E: 4.924234 rate D <-> G: 0.793424 rate D <-> H: 0.870603 rate D <-> I: 0.010038 rate D <-> L: 0.014157 rate D <-> K: 0.265711 rate D <-> M: 0.023991 rate D <-> F: 0.016354 rate D <-> P: 0.370412 rate D <-> S: 1.164675 rate D <-> T: 0.399902 rate D <-> W: 0.028068 rate D <-> Y: 0.126872 rate D <-> V: 0.035653 rate C <-> Q: 0.079639 rate C <-> E: 0.003286 rate C <-> G: 0.534566 rate C <-> H: 0.601499 rate C <-> I: 0.301083 rate C <-> L: 0.557800 rate C <-> K: 0.012457 rate C <-> M: 0.839207 rate C <-> F: 1.037881 rate C <-> P: 0.070787 rate C <-> S: 2.614753 rate C <-> T: 1.073780 rate C <-> W: 0.629281 rate C <-> Y: 1.094488 rate C <-> V: 1.839864 rate Q <-> E: 3.876936 rate Q <-> G: 0.251626 rate Q <-> H: 4.520102 rate Q <-> I: 0.068413 rate Q <-> L: 0.546954 rate Q <-> K: 3.037150 rate Q <-> M: 1.570619 rate Q <-> F: 0.033669 rate Q <-> P: 0.586241 rate Q <-> S: 1.149231 rate Q <-> T: 1.014297 rate Q <-> W: 0.221802 rate Q <-> Y: 0.241650 rate Q <-> V: 0.197511 rate E <-> G: 0.327583 rate E <-> H: 0.398044 rate E <-> I: 0.041567 rate E <-> L: 0.065426 rate E <-> K: 1.697022 rate E <-> M: 0.163145 rate E <-> F: 0.017664 rate E <-> P: 0.393844 rate E <-> S: 0.574671 rate E <-> T: 0.567695 rate E <-> W: 0.073107 rate E <-> Y: 0.112720 rate E <-> V: 0.230098 rate G <-> H: 0.292498 rate G <-> I: 0.008174 rate G <-> L: 0.041563 rate G <-> K: 0.278555 rate G <-> M: 0.131033 rate G <-> F: 0.084125 rate G <-> P: 0.184955 rate G <-> S: 1.633930 rate G <-> T: 0.121922 rate G <-> W: 0.252125 rate G <-> Y: 0.051346 rate G <-> V: 0.072026 rate H <-> I: 0.102245 rate H <-> L: 0.343988 rate H <-> K: 0.654763 rate H <-> M: 0.415502 rate H <-> F: 0.640560 rate H <-> P: 0.477834 rate H <-> S: 0.929667 rate H <-> T: 0.548649 rate H <-> W: 0.560661 rate H <-> Y: 4.983361 rate H <-> V: 0.111759 rate I <-> L: 3.892408 rate I <-> K: 0.149373 rate I <-> M: 4.013113 rate I <-> F: 1.044902 rate I <-> P: 0.073509 rate I <-> S: 0.060198 rate I <-> T: 0.970728 rate I <-> W: 0.104854 rate I <-> Y: 0.218350 rate I <-> V: 10.000000 rate L <-> K: 0.129119 rate L <-> M: 5.927594 rate L <-> F: 2.434657 rate L <-> P: 0.233879 rate L <-> S: 0.171176 rate L <-> T: 0.284471 rate L <-> W: 0.581863 rate L <-> Y: 0.281383 rate L <-> V: 1.598956 rate K <-> M: 0.616581 rate K <-> F: 0.022460 rate K <-> P: 0.366530 rate K <-> S: 0.703048 rate K <-> T: 1.067567 rate K <-> W: 0.046864 rate K <-> Y: 0.123890 rate K <-> V: 0.173913 rate M <-> F: 1.689205 rate M <-> P: 0.093763 rate M <-> S: 0.325811 rate M <-> T: 1.897216 rate M <-> W: 0.653740 rate M <-> Y: 0.451968 rate M <-> V: 1.782983 rate F <-> P: 0.088706 rate F <-> S: 0.339765 rate F <-> T: 0.154944 rate F <-> W: 2.307349 rate F <-> Y: 7.328222 rate F <-> V: 0.614777 rate P <-> S: 1.256567 rate P <-> T: 0.536635 rate P <-> W: 0.089332 rate P <-> Y: 0.084151 rate P <-> V: 0.278428 rate S <-> T: 6.077767 rate S <-> W: 0.233693 rate S <-> Y: 0.376132 rate S <-> V: 0.092373 rate T <-> W: 0.132241 rate T <-> Y: 0.230856 rate T <-> V: 2.054781 rate W <-> Y: 2.959699 rate W <-> V: 0.177959 rate Y <-> V: 0.234116 freq pi(A): 0.079060 freq pi(R): 0.055940 freq pi(N): 0.041980 freq pi(D): 0.053050 freq pi(C): 0.012940 freq pi(Q): 0.040770 freq pi(E): 0.071580 freq pi(G): 0.057340 freq pi(H): 0.022350 freq pi(I): 0.062160 freq pi(L): 0.099080 freq pi(K): 0.064600 freq pi(M): 0.022950 freq pi(F): 0.042300 freq pi(P): 0.044040 freq pi(S): 0.061200 freq pi(T): 0.053290 freq pi(W): 0.012070 freq pi(Y): 0.034150 freq pi(V): 0.069150 ML search took 372.283728 secs or 0.103412 hours Combined Bootstrap and ML search took 613.611527 secs or 0.170448 hours Drawing Bootstrap Support Values on best-scoring ML tree ... Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Scrippsiella-hangoei_like-SHHI_4.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Scrippsiella-hangoei_like-SHHI_4.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Scrippsiella-hangoei_like-SHHI_4.MUSCLE All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.Scrippsiella-hangoei_like-SHHI_4.MUSCLE Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Scrippsiella-hangoei_like-SHHI_4.MUSCLE Best-scoring ML tree with support values written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bipartitions.Scrippsiella-hangoei_like-SHHI_4.MUSCLE Best-scoring ML tree with support values as branch labels written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bipartitionsBranchLabels.Scrippsiella-hangoei_like-SHHI_4.MUSCLE Overall execution time for full ML analysis: 613.624434 secs or 0.170451 hours or 0.007102 days