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 262 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 72.20% 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: 262 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Pelagodinium-beii-RCC1491.MUSCLE.fa -n Pelagodinium-beii-RCC1491.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.088668 Bootstrap[0]: Time 2.529217 seconds, bootstrap likelihood -7603.743673, best rearrangement setting 13 Bootstrap[1]: Time 2.007361 seconds, bootstrap likelihood -7297.206106, best rearrangement setting 13 Bootstrap[2]: Time 2.644250 seconds, bootstrap likelihood -8660.505392, best rearrangement setting 12 Bootstrap[3]: Time 2.607461 seconds, bootstrap likelihood -6741.956973, best rearrangement setting 15 Bootstrap[4]: Time 2.526802 seconds, bootstrap likelihood -7294.624764, best rearrangement setting 10 Bootstrap[5]: Time 2.793287 seconds, bootstrap likelihood -7856.353451, best rearrangement setting 10 Bootstrap[6]: Time 3.112182 seconds, bootstrap likelihood -7483.278101, best rearrangement setting 6 Bootstrap[7]: Time 2.733283 seconds, bootstrap likelihood -7855.889969, best rearrangement setting 14 Bootstrap[8]: Time 2.800356 seconds, bootstrap likelihood -7694.880529, best rearrangement setting 5 Bootstrap[9]: Time 2.573319 seconds, bootstrap likelihood -7042.523824, best rearrangement setting 7 Bootstrap[10]: Time 2.642510 seconds, bootstrap likelihood -7379.183984, best rearrangement setting 7 Bootstrap[11]: Time 2.450555 seconds, bootstrap likelihood -6966.139305, best rearrangement setting 5 Bootstrap[12]: Time 2.261932 seconds, bootstrap likelihood -6871.272140, best rearrangement setting 8 Bootstrap[13]: Time 2.573570 seconds, bootstrap likelihood -7512.941651, best rearrangement setting 7 Bootstrap[14]: Time 2.613478 seconds, bootstrap likelihood -7832.015576, best rearrangement setting 12 Bootstrap[15]: Time 2.455951 seconds, bootstrap likelihood -7286.360999, best rearrangement setting 15 Bootstrap[16]: Time 2.256778 seconds, bootstrap likelihood -6886.012056, best rearrangement setting 12 Bootstrap[17]: Time 2.478766 seconds, bootstrap likelihood -7793.612445, best rearrangement setting 12 Bootstrap[18]: Time 2.363835 seconds, bootstrap likelihood -7335.291550, best rearrangement setting 5 Bootstrap[19]: Time 2.722702 seconds, bootstrap likelihood -6874.997398, best rearrangement setting 8 Bootstrap[20]: Time 2.369256 seconds, bootstrap likelihood -7609.729645, best rearrangement setting 10 Bootstrap[21]: Time 2.338296 seconds, bootstrap likelihood -7207.357069, best rearrangement setting 6 Bootstrap[22]: Time 2.405182 seconds, bootstrap likelihood -7360.605364, best rearrangement setting 5 Bootstrap[23]: Time 2.505255 seconds, bootstrap likelihood -6603.409590, best rearrangement setting 7 Bootstrap[24]: Time 2.773442 seconds, bootstrap likelihood -7269.119525, best rearrangement setting 8 Bootstrap[25]: Time 2.305968 seconds, bootstrap likelihood -7831.922449, best rearrangement setting 6 Bootstrap[26]: Time 2.448599 seconds, bootstrap likelihood -7736.449684, best rearrangement setting 12 Bootstrap[27]: Time 2.418619 seconds, bootstrap likelihood -7117.809930, best rearrangement setting 10 Bootstrap[28]: Time 2.564949 seconds, bootstrap likelihood -6027.907496, best rearrangement setting 11 Bootstrap[29]: Time 2.444120 seconds, bootstrap likelihood -8136.635710, best rearrangement setting 12 Bootstrap[30]: Time 2.500196 seconds, bootstrap likelihood -7808.592561, best rearrangement setting 15 Bootstrap[31]: Time 2.241712 seconds, bootstrap likelihood -7470.194515, best rearrangement setting 15 Bootstrap[32]: Time 2.738584 seconds, bootstrap likelihood -7065.537008, best rearrangement setting 6 Bootstrap[33]: Time 2.627640 seconds, bootstrap likelihood -7153.841014, best rearrangement setting 15 Bootstrap[34]: Time 2.506916 seconds, bootstrap likelihood -7538.055686, best rearrangement setting 11 Bootstrap[35]: Time 2.140890 seconds, bootstrap likelihood -7419.794102, best rearrangement setting 8 Bootstrap[36]: Time 2.618604 seconds, bootstrap likelihood -6679.362057, best rearrangement setting 9 Bootstrap[37]: Time 2.781353 seconds, bootstrap likelihood -7657.656214, best rearrangement setting 11 Bootstrap[38]: Time 2.722621 seconds, bootstrap likelihood -7578.223968, best rearrangement setting 8 Bootstrap[39]: Time 2.684545 seconds, bootstrap likelihood -7985.502456, best rearrangement setting 13 Bootstrap[40]: Time 2.692066 seconds, bootstrap likelihood -7361.822784, best rearrangement setting 13 Bootstrap[41]: Time 2.559111 seconds, bootstrap likelihood -7732.491179, best rearrangement setting 10 Bootstrap[42]: Time 2.191908 seconds, bootstrap likelihood -6754.595560, best rearrangement setting 5 Bootstrap[43]: Time 2.719376 seconds, bootstrap likelihood -7061.042078, best rearrangement setting 14 Bootstrap[44]: Time 2.861450 seconds, bootstrap likelihood -7510.535478, best rearrangement setting 10 Bootstrap[45]: Time 2.395770 seconds, bootstrap likelihood -7946.369396, best rearrangement setting 15 Bootstrap[46]: Time 2.142082 seconds, bootstrap likelihood -7455.408326, best rearrangement setting 14 Bootstrap[47]: Time 2.864963 seconds, bootstrap likelihood -6766.687268, best rearrangement setting 8 Bootstrap[48]: Time 2.936880 seconds, bootstrap likelihood -7718.956356, best rearrangement setting 6 Bootstrap[49]: Time 2.787158 seconds, bootstrap likelihood -8657.114629, best rearrangement setting 7 Bootstrap[50]: Time 2.555879 seconds, bootstrap likelihood -8394.261406, best rearrangement setting 7 Bootstrap[51]: Time 2.273271 seconds, bootstrap likelihood -6894.168572, best rearrangement setting 11 Bootstrap[52]: Time 2.799459 seconds, bootstrap likelihood -6913.727388, best rearrangement setting 12 Bootstrap[53]: Time 2.814987 seconds, bootstrap likelihood -8158.662474, best rearrangement setting 8 Bootstrap[54]: Time 3.110158 seconds, bootstrap likelihood -7705.025056, best rearrangement setting 9 Bootstrap[55]: Time 2.363767 seconds, bootstrap likelihood -6906.609575, best rearrangement setting 11 Bootstrap[56]: Time 2.477358 seconds, bootstrap likelihood -7029.993661, best rearrangement setting 5 Bootstrap[57]: Time 2.674572 seconds, bootstrap likelihood -7519.459606, best rearrangement setting 7 Bootstrap[58]: Time 2.740630 seconds, bootstrap likelihood -7366.335814, best rearrangement setting 10 Bootstrap[59]: Time 2.641844 seconds, bootstrap likelihood -7907.100739, best rearrangement setting 9 Bootstrap[60]: Time 2.667036 seconds, bootstrap likelihood -7106.286378, best rearrangement setting 7 Bootstrap[61]: Time 2.342301 seconds, bootstrap likelihood -7202.458179, best rearrangement setting 5 Bootstrap[62]: Time 2.715285 seconds, bootstrap likelihood -6943.778358, best rearrangement setting 11 Bootstrap[63]: Time 2.683537 seconds, bootstrap likelihood -7638.811376, best rearrangement setting 12 Bootstrap[64]: Time 2.813093 seconds, bootstrap likelihood -7385.464288, best rearrangement setting 7 Bootstrap[65]: Time 2.866930 seconds, bootstrap likelihood -7118.027921, best rearrangement setting 5 Bootstrap[66]: Time 2.651197 seconds, bootstrap likelihood -7634.221144, best rearrangement setting 5 Bootstrap[67]: Time 2.754515 seconds, bootstrap likelihood -7862.885028, best rearrangement setting 15 Bootstrap[68]: Time 2.493425 seconds, bootstrap likelihood -7249.250199, best rearrangement setting 11 Bootstrap[69]: Time 2.601873 seconds, bootstrap likelihood -7878.750902, best rearrangement setting 5 Bootstrap[70]: Time 2.615293 seconds, bootstrap likelihood -6806.784659, best rearrangement setting 8 Bootstrap[71]: Time 2.851711 seconds, bootstrap likelihood -7657.376571, best rearrangement setting 10 Bootstrap[72]: Time 2.699435 seconds, bootstrap likelihood -7143.257516, best rearrangement setting 11 Bootstrap[73]: Time 2.714306 seconds, bootstrap likelihood -7143.794581, best rearrangement setting 9 Bootstrap[74]: Time 1.967617 seconds, bootstrap likelihood -7322.523527, best rearrangement setting 5 Bootstrap[75]: Time 2.143510 seconds, bootstrap likelihood -7843.188622, best rearrangement setting 8 Bootstrap[76]: Time 2.298570 seconds, bootstrap likelihood -8433.506751, best rearrangement setting 9 Bootstrap[77]: Time 2.598513 seconds, bootstrap likelihood -8814.611662, best rearrangement setting 11 Bootstrap[78]: Time 2.393555 seconds, bootstrap likelihood -7420.800916, best rearrangement setting 15 Bootstrap[79]: Time 2.398587 seconds, bootstrap likelihood -8033.670753, best rearrangement setting 9 Bootstrap[80]: Time 2.805921 seconds, bootstrap likelihood -8002.923788, best rearrangement setting 15 Bootstrap[81]: Time 2.338194 seconds, bootstrap likelihood -7652.858972, best rearrangement setting 7 Bootstrap[82]: Time 2.337583 seconds, bootstrap likelihood -7415.391612, best rearrangement setting 6 Bootstrap[83]: Time 2.779157 seconds, bootstrap likelihood -7230.315944, best rearrangement setting 10 Bootstrap[84]: Time 3.119083 seconds, bootstrap likelihood -7335.928094, best rearrangement setting 11 Bootstrap[85]: Time 2.499602 seconds, bootstrap likelihood -6729.671063, best rearrangement setting 8 Bootstrap[86]: Time 2.546125 seconds, bootstrap likelihood -7941.995469, best rearrangement setting 7 Bootstrap[87]: Time 2.498274 seconds, bootstrap likelihood -7325.784259, best rearrangement setting 7 Bootstrap[88]: Time 2.752548 seconds, bootstrap likelihood -7563.361824, best rearrangement setting 12 Bootstrap[89]: Time 2.846048 seconds, bootstrap likelihood -6732.622241, best rearrangement setting 10 Bootstrap[90]: Time 2.504443 seconds, bootstrap likelihood -7912.550646, best rearrangement setting 8 Bootstrap[91]: Time 2.510535 seconds, bootstrap likelihood -7929.568881, best rearrangement setting 12 Bootstrap[92]: Time 2.884273 seconds, bootstrap likelihood -7273.413235, best rearrangement setting 13 Bootstrap[93]: Time 3.418322 seconds, bootstrap likelihood -8071.499601, best rearrangement setting 15 Bootstrap[94]: Time 3.031884 seconds, bootstrap likelihood -6355.973283, best rearrangement setting 5 Bootstrap[95]: Time 2.567249 seconds, bootstrap likelihood -7330.278329, best rearrangement setting 5 Bootstrap[96]: Time 2.632739 seconds, bootstrap likelihood -7044.729541, best rearrangement setting 13 Bootstrap[97]: Time 2.227887 seconds, bootstrap likelihood -7540.894500, best rearrangement setting 11 Bootstrap[98]: Time 2.212950 seconds, bootstrap likelihood -6837.294254, best rearrangement setting 6 Bootstrap[99]: Time 2.419096 seconds, bootstrap likelihood -7009.962462, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 258.166639 seconds Average Time per Rapid Bootstrap 2.581666 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 255.889366 seconds Slow ML Search 0 Likelihood: -7493.677682 Slow ML Search 1 Likelihood: -7493.677684 Slow ML Search 2 Likelihood: -7493.677684 Slow ML Search 3 Likelihood: -7493.677684 Slow ML Search 4 Likelihood: -7493.677684 Slow ML Search 5 Likelihood: -7493.677684 Slow ML Search 6 Likelihood: -7493.677693 Slow ML Search 7 Likelihood: -7493.677693 Slow ML Search 8 Likelihood: -7493.849180 Slow ML Search 9 Likelihood: -7493.849187 Slow ML optimization finished Slow ML search Time: 92.627538 seconds Thorough ML search Time: 10.629440 seconds Final ML Optimization Likelihood: -7493.678261 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.127791 Tree-Length: 41.455531 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 359.234454 secs or 0.099787 hours Combined Bootstrap and ML search took 617.401889 secs or 0.171501 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.Pelagodinium-beii-RCC1491.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Pelagodinium-beii-RCC1491.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Pelagodinium-beii-RCC1491.MUSCLE All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.Pelagodinium-beii-RCC1491.MUSCLE Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Pelagodinium-beii-RCC1491.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.Pelagodinium-beii-RCC1491.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.Pelagodinium-beii-RCC1491.MUSCLE Overall execution time for full ML analysis: 617.415831 secs or 0.171504 hours or 0.007146 days