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 293 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 71.32% 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: 293 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Karlodinium-micrum-CCMP2283.MUSCLE.fa -n Karlodinium-micrum-CCMP2283.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.174243 Bootstrap[0]: Time 2.645854 seconds, bootstrap likelihood -8131.221020, best rearrangement setting 13 Bootstrap[1]: Time 2.398262 seconds, bootstrap likelihood -7361.503792, best rearrangement setting 13 Bootstrap[2]: Time 2.581162 seconds, bootstrap likelihood -8424.726668, best rearrangement setting 12 Bootstrap[3]: Time 2.530406 seconds, bootstrap likelihood -7126.802129, best rearrangement setting 15 Bootstrap[4]: Time 2.510752 seconds, bootstrap likelihood -7599.853715, best rearrangement setting 10 Bootstrap[5]: Time 2.547874 seconds, bootstrap likelihood -8180.123058, best rearrangement setting 10 Bootstrap[6]: Time 2.505154 seconds, bootstrap likelihood -8104.607744, best rearrangement setting 6 Bootstrap[7]: Time 2.156915 seconds, bootstrap likelihood -8077.893572, best rearrangement setting 14 Bootstrap[8]: Time 2.403886 seconds, bootstrap likelihood -8457.969750, best rearrangement setting 5 Bootstrap[9]: Time 2.303727 seconds, bootstrap likelihood -7743.905330, best rearrangement setting 7 Bootstrap[10]: Time 2.457250 seconds, bootstrap likelihood -7619.842852, best rearrangement setting 7 Bootstrap[11]: Time 2.732501 seconds, bootstrap likelihood -7592.840044, best rearrangement setting 5 Bootstrap[12]: Time 2.182966 seconds, bootstrap likelihood -7069.340345, best rearrangement setting 8 Bootstrap[13]: Time 2.794204 seconds, bootstrap likelihood -7645.466696, best rearrangement setting 7 Bootstrap[14]: Time 2.300791 seconds, bootstrap likelihood -7761.126543, best rearrangement setting 12 Bootstrap[15]: Time 2.834684 seconds, bootstrap likelihood -7540.867501, best rearrangement setting 15 Bootstrap[16]: Time 2.803504 seconds, bootstrap likelihood -7580.620390, best rearrangement setting 12 Bootstrap[17]: Time 2.511239 seconds, bootstrap likelihood -8064.811035, best rearrangement setting 12 Bootstrap[18]: Time 2.714156 seconds, bootstrap likelihood -8094.440318, best rearrangement setting 5 Bootstrap[19]: Time 2.433622 seconds, bootstrap likelihood -7028.537623, best rearrangement setting 8 Bootstrap[20]: Time 2.245450 seconds, bootstrap likelihood -7731.478401, best rearrangement setting 10 Bootstrap[21]: Time 2.439123 seconds, bootstrap likelihood -7410.093516, best rearrangement setting 6 Bootstrap[22]: Time 2.476189 seconds, bootstrap likelihood -7722.345933, best rearrangement setting 5 Bootstrap[23]: Time 2.485871 seconds, bootstrap likelihood -7734.539543, best rearrangement setting 7 Bootstrap[24]: Time 2.901545 seconds, bootstrap likelihood -7779.884686, best rearrangement setting 8 Bootstrap[25]: Time 2.178850 seconds, bootstrap likelihood -8217.203744, best rearrangement setting 6 Bootstrap[26]: Time 1.917143 seconds, bootstrap likelihood -7950.053698, best rearrangement setting 12 Bootstrap[27]: Time 2.544510 seconds, bootstrap likelihood -8156.741424, best rearrangement setting 10 Bootstrap[28]: Time 2.320097 seconds, bootstrap likelihood -7262.168953, best rearrangement setting 11 Bootstrap[29]: Time 2.571897 seconds, bootstrap likelihood -8103.443070, best rearrangement setting 12 Bootstrap[30]: Time 2.448762 seconds, bootstrap likelihood -8125.668029, best rearrangement setting 15 Bootstrap[31]: Time 2.333454 seconds, bootstrap likelihood -8236.405157, best rearrangement setting 15 Bootstrap[32]: Time 2.517771 seconds, bootstrap likelihood -6934.911824, best rearrangement setting 6 Bootstrap[33]: Time 2.133987 seconds, bootstrap likelihood -7536.859466, best rearrangement setting 15 Bootstrap[34]: Time 2.373335 seconds, bootstrap likelihood -8048.813671, best rearrangement setting 11 Bootstrap[35]: Time 2.239700 seconds, bootstrap likelihood -7893.626779, best rearrangement setting 8 Bootstrap[36]: Time 2.424829 seconds, bootstrap likelihood -7319.549234, best rearrangement setting 9 Bootstrap[37]: Time 2.401867 seconds, bootstrap likelihood -8237.816285, best rearrangement setting 11 Bootstrap[38]: Time 2.401984 seconds, bootstrap likelihood -8063.885288, best rearrangement setting 8 Bootstrap[39]: Time 2.512214 seconds, bootstrap likelihood -7906.311246, best rearrangement setting 13 Bootstrap[40]: Time 2.358053 seconds, bootstrap likelihood -7722.881842, best rearrangement setting 13 Bootstrap[41]: Time 2.699483 seconds, bootstrap likelihood -8177.011523, best rearrangement setting 10 Bootstrap[42]: Time 2.381469 seconds, bootstrap likelihood -7190.642468, best rearrangement setting 5 Bootstrap[43]: Time 2.485281 seconds, bootstrap likelihood -7559.915311, best rearrangement setting 14 Bootstrap[44]: Time 2.734485 seconds, bootstrap likelihood -7759.061966, best rearrangement setting 10 Bootstrap[45]: Time 2.833673 seconds, bootstrap likelihood -8791.313922, best rearrangement setting 15 Bootstrap[46]: Time 2.390592 seconds, bootstrap likelihood -7639.635119, best rearrangement setting 14 Bootstrap[47]: Time 2.539062 seconds, bootstrap likelihood -7115.264161, best rearrangement setting 8 Bootstrap[48]: Time 2.542357 seconds, bootstrap likelihood -7868.537456, best rearrangement setting 6 Bootstrap[49]: Time 2.318874 seconds, bootstrap likelihood -8106.338399, best rearrangement setting 7 Bootstrap[50]: Time 2.445574 seconds, bootstrap likelihood -8408.059238, best rearrangement setting 7 Bootstrap[51]: Time 2.729700 seconds, bootstrap likelihood -7083.271570, best rearrangement setting 11 Bootstrap[52]: Time 2.320898 seconds, bootstrap likelihood -7740.258036, best rearrangement setting 12 Bootstrap[53]: Time 2.364430 seconds, bootstrap likelihood -7985.603422, best rearrangement setting 8 Bootstrap[54]: Time 2.418430 seconds, bootstrap likelihood -8242.366771, best rearrangement setting 9 Bootstrap[55]: Time 2.352705 seconds, bootstrap likelihood -7415.657807, best rearrangement setting 11 Bootstrap[56]: Time 2.491151 seconds, bootstrap likelihood -8152.157058, best rearrangement setting 5 Bootstrap[57]: Time 2.522597 seconds, bootstrap likelihood -8179.048525, best rearrangement setting 7 Bootstrap[58]: Time 2.598661 seconds, bootstrap likelihood -7461.075904, best rearrangement setting 10 Bootstrap[59]: Time 2.896982 seconds, bootstrap likelihood -7602.513283, best rearrangement setting 9 Bootstrap[60]: Time 2.170207 seconds, bootstrap likelihood -7774.834314, best rearrangement setting 7 Bootstrap[61]: Time 2.411981 seconds, bootstrap likelihood -8089.821469, best rearrangement setting 5 Bootstrap[62]: Time 2.558400 seconds, bootstrap likelihood -6996.611388, best rearrangement setting 11 Bootstrap[63]: Time 2.810531 seconds, bootstrap likelihood -7598.550249, best rearrangement setting 12 Bootstrap[64]: Time 2.617886 seconds, bootstrap likelihood -8259.158721, best rearrangement setting 7 Bootstrap[65]: Time 2.302012 seconds, bootstrap likelihood -7086.744440, best rearrangement setting 5 Bootstrap[66]: Time 2.423340 seconds, bootstrap likelihood -8541.730961, best rearrangement setting 5 Bootstrap[67]: Time 2.391864 seconds, bootstrap likelihood -8061.413073, best rearrangement setting 15 Bootstrap[68]: Time 2.225358 seconds, bootstrap likelihood -7346.457860, best rearrangement setting 11 Bootstrap[69]: Time 2.315765 seconds, bootstrap likelihood -8223.094468, best rearrangement setting 5 Bootstrap[70]: Time 2.560960 seconds, bootstrap likelihood -7378.134817, best rearrangement setting 8 Bootstrap[71]: Time 3.004595 seconds, bootstrap likelihood -7880.830494, best rearrangement setting 10 Bootstrap[72]: Time 2.076488 seconds, bootstrap likelihood -7375.039083, best rearrangement setting 11 Bootstrap[73]: Time 2.773451 seconds, bootstrap likelihood -7194.495420, best rearrangement setting 9 Bootstrap[74]: Time 2.578783 seconds, bootstrap likelihood -7290.303313, best rearrangement setting 5 Bootstrap[75]: Time 2.548664 seconds, bootstrap likelihood -7515.284264, best rearrangement setting 8 Bootstrap[76]: Time 2.739692 seconds, bootstrap likelihood -8567.232113, best rearrangement setting 9 Bootstrap[77]: Time 2.219910 seconds, bootstrap likelihood -8500.621306, best rearrangement setting 11 Bootstrap[78]: Time 2.619395 seconds, bootstrap likelihood -8237.209329, best rearrangement setting 15 Bootstrap[79]: Time 2.710555 seconds, bootstrap likelihood -8419.921557, best rearrangement setting 9 Bootstrap[80]: Time 2.521227 seconds, bootstrap likelihood -8610.683146, best rearrangement setting 15 Bootstrap[81]: Time 2.224969 seconds, bootstrap likelihood -7778.046516, best rearrangement setting 7 Bootstrap[82]: Time 2.510163 seconds, bootstrap likelihood -8065.362830, best rearrangement setting 6 Bootstrap[83]: Time 2.296529 seconds, bootstrap likelihood -7663.992108, best rearrangement setting 10 Bootstrap[84]: Time 2.436750 seconds, bootstrap likelihood -7434.533723, best rearrangement setting 11 Bootstrap[85]: Time 2.417052 seconds, bootstrap likelihood -7419.147012, best rearrangement setting 8 Bootstrap[86]: Time 2.785442 seconds, bootstrap likelihood -8199.917211, best rearrangement setting 7 Bootstrap[87]: Time 2.868931 seconds, bootstrap likelihood -7156.102270, best rearrangement setting 7 Bootstrap[88]: Time 2.978691 seconds, bootstrap likelihood -8274.668756, best rearrangement setting 12 Bootstrap[89]: Time 2.555792 seconds, bootstrap likelihood -7187.036134, best rearrangement setting 10 Bootstrap[90]: Time 2.436164 seconds, bootstrap likelihood -7985.189708, best rearrangement setting 8 Bootstrap[91]: Time 2.466408 seconds, bootstrap likelihood -8680.167119, best rearrangement setting 12 Bootstrap[92]: Time 2.223556 seconds, bootstrap likelihood -7552.378208, best rearrangement setting 13 Bootstrap[93]: Time 2.598681 seconds, bootstrap likelihood -8279.976740, best rearrangement setting 15 Bootstrap[94]: Time 2.780549 seconds, bootstrap likelihood -7106.067999, best rearrangement setting 5 Bootstrap[95]: Time 2.425981 seconds, bootstrap likelihood -7730.997308, best rearrangement setting 5 Bootstrap[96]: Time 2.972565 seconds, bootstrap likelihood -7585.635266, best rearrangement setting 13 Bootstrap[97]: Time 2.829879 seconds, bootstrap likelihood -7804.530229, best rearrangement setting 11 Bootstrap[98]: Time 2.418412 seconds, bootstrap likelihood -6921.409477, best rearrangement setting 6 Bootstrap[99]: Time 2.449102 seconds, bootstrap likelihood -7946.511994, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 249.983556 seconds Average Time per Rapid Bootstrap 2.499836 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 343.534692 seconds Slow ML Search 0 Likelihood: -7815.353563 Slow ML Search 1 Likelihood: -7815.353563 Slow ML Search 2 Likelihood: -7815.353563 Slow ML Search 3 Likelihood: -7815.353563 Slow ML Search 4 Likelihood: -7815.353563 Slow ML Search 5 Likelihood: -7815.353563 Slow ML Search 6 Likelihood: -7815.353563 Slow ML Search 7 Likelihood: -7815.353563 Slow ML Search 8 Likelihood: -7815.353563 Slow ML Search 9 Likelihood: -7815.353563 Slow ML optimization finished Slow ML search Time: 80.683292 seconds Thorough ML search Time: 12.589096 seconds Final ML Optimization Likelihood: -7815.353995 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.447752 Tree-Length: 33.059080 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 436.894413 secs or 0.121360 hours Combined Bootstrap and ML search took 686.878784 secs or 0.190800 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.Karlodinium-micrum-CCMP2283.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Karlodinium-micrum-CCMP2283.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Karlodinium-micrum-CCMP2283.MUSCLE All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.Karlodinium-micrum-CCMP2283.MUSCLE Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Karlodinium-micrum-CCMP2283.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.Karlodinium-micrum-CCMP2283.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.Karlodinium-micrum-CCMP2283.MUSCLE Overall execution time for full ML analysis: 686.892476 secs or 0.190803 hours or 0.007950 days