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 359 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 74.17% 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: 359 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Noctiluca-scintillans-Unknown.MUSCLE.fa -n Noctiluca-scintillans-Unknown.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.111106 Bootstrap[0]: Time 4.166476 seconds, bootstrap likelihood -8336.101398, best rearrangement setting 13 Bootstrap[1]: Time 3.407858 seconds, bootstrap likelihood -9062.897619, best rearrangement setting 13 Bootstrap[2]: Time 3.792544 seconds, bootstrap likelihood -8474.199581, best rearrangement setting 12 Bootstrap[3]: Time 3.488757 seconds, bootstrap likelihood -8030.015138, best rearrangement setting 15 Bootstrap[4]: Time 3.197177 seconds, bootstrap likelihood -9498.327022, best rearrangement setting 10 Bootstrap[5]: Time 2.677541 seconds, bootstrap likelihood -8615.608985, best rearrangement setting 10 Bootstrap[6]: Time 3.142893 seconds, bootstrap likelihood -9393.360983, best rearrangement setting 6 Bootstrap[7]: Time 3.169613 seconds, bootstrap likelihood -8470.537328, best rearrangement setting 14 Bootstrap[8]: Time 3.712528 seconds, bootstrap likelihood -9386.554625, best rearrangement setting 5 Bootstrap[9]: Time 3.383649 seconds, bootstrap likelihood -8299.746063, best rearrangement setting 7 Bootstrap[10]: Time 3.262814 seconds, bootstrap likelihood -8106.269116, best rearrangement setting 7 Bootstrap[11]: Time 3.632130 seconds, bootstrap likelihood -7922.897295, best rearrangement setting 5 Bootstrap[12]: Time 4.015393 seconds, bootstrap likelihood -9146.325097, best rearrangement setting 8 Bootstrap[13]: Time 3.257770 seconds, bootstrap likelihood -8215.028415, best rearrangement setting 7 Bootstrap[14]: Time 3.313059 seconds, bootstrap likelihood -8244.457345, best rearrangement setting 12 Bootstrap[15]: Time 3.870212 seconds, bootstrap likelihood -9167.308790, best rearrangement setting 15 Bootstrap[16]: Time 3.321773 seconds, bootstrap likelihood -8453.647863, best rearrangement setting 12 Bootstrap[17]: Time 3.900147 seconds, bootstrap likelihood -8312.305085, best rearrangement setting 12 Bootstrap[18]: Time 3.297640 seconds, bootstrap likelihood -7853.058106, best rearrangement setting 5 Bootstrap[19]: Time 3.181656 seconds, bootstrap likelihood -8105.482181, best rearrangement setting 8 Bootstrap[20]: Time 2.958274 seconds, bootstrap likelihood -8901.706139, best rearrangement setting 10 Bootstrap[21]: Time 3.213374 seconds, bootstrap likelihood -8350.809734, best rearrangement setting 6 Bootstrap[22]: Time 3.530712 seconds, bootstrap likelihood -8173.445016, best rearrangement setting 5 Bootstrap[23]: Time 3.399695 seconds, bootstrap likelihood -8664.184057, best rearrangement setting 7 Bootstrap[24]: Time 3.704924 seconds, bootstrap likelihood -8436.019718, best rearrangement setting 8 Bootstrap[25]: Time 3.452180 seconds, bootstrap likelihood -7435.421321, best rearrangement setting 6 Bootstrap[26]: Time 3.349857 seconds, bootstrap likelihood -8731.183195, best rearrangement setting 12 Bootstrap[27]: Time 3.695774 seconds, bootstrap likelihood -9036.562739, best rearrangement setting 10 Bootstrap[28]: Time 3.471845 seconds, bootstrap likelihood -7956.051713, best rearrangement setting 11 Bootstrap[29]: Time 3.823365 seconds, bootstrap likelihood -8415.134359, best rearrangement setting 12 Bootstrap[30]: Time 3.620866 seconds, bootstrap likelihood -8768.662272, best rearrangement setting 15 Bootstrap[31]: Time 3.153668 seconds, bootstrap likelihood -8443.308664, best rearrangement setting 15 Bootstrap[32]: Time 3.031223 seconds, bootstrap likelihood -7878.953956, best rearrangement setting 6 Bootstrap[33]: Time 3.653266 seconds, bootstrap likelihood -8847.259287, best rearrangement setting 15 Bootstrap[34]: Time 4.066869 seconds, bootstrap likelihood -8874.823811, best rearrangement setting 11 Bootstrap[35]: Time 3.316645 seconds, bootstrap likelihood -8674.569421, best rearrangement setting 8 Bootstrap[36]: Time 3.039211 seconds, bootstrap likelihood -8367.882475, best rearrangement setting 9 Bootstrap[37]: Time 3.066843 seconds, bootstrap likelihood -9448.235591, best rearrangement setting 11 Bootstrap[38]: Time 3.417045 seconds, bootstrap likelihood -8585.059734, best rearrangement setting 8 Bootstrap[39]: Time 3.538397 seconds, bootstrap likelihood -8708.991721, best rearrangement setting 13 Bootstrap[40]: Time 3.549814 seconds, bootstrap likelihood -9029.230541, best rearrangement setting 13 Bootstrap[41]: Time 3.712355 seconds, bootstrap likelihood -8837.932702, best rearrangement setting 10 Bootstrap[42]: Time 3.008015 seconds, bootstrap likelihood -8360.310796, best rearrangement setting 5 Bootstrap[43]: Time 4.208964 seconds, bootstrap likelihood -8329.866844, best rearrangement setting 14 Bootstrap[44]: Time 4.359844 seconds, bootstrap likelihood -9822.678046, best rearrangement setting 10 Bootstrap[45]: Time 3.259009 seconds, bootstrap likelihood -9076.227360, best rearrangement setting 15 Bootstrap[46]: Time 3.757623 seconds, bootstrap likelihood -8626.449327, best rearrangement setting 14 Bootstrap[47]: Time 3.694024 seconds, bootstrap likelihood -8786.773326, best rearrangement setting 8 Bootstrap[48]: Time 3.290454 seconds, bootstrap likelihood -8585.222695, best rearrangement setting 6 Bootstrap[49]: Time 3.019700 seconds, bootstrap likelihood -8192.787447, best rearrangement setting 7 Bootstrap[50]: Time 3.118547 seconds, bootstrap likelihood -9206.686270, best rearrangement setting 7 Bootstrap[51]: Time 3.578333 seconds, bootstrap likelihood -8076.819167, best rearrangement setting 11 Bootstrap[52]: Time 3.667597 seconds, bootstrap likelihood -8769.871363, best rearrangement setting 12 Bootstrap[53]: Time 3.429368 seconds, bootstrap likelihood -8367.552720, best rearrangement setting 8 Bootstrap[54]: Time 3.799584 seconds, bootstrap likelihood -8507.531838, best rearrangement setting 9 Bootstrap[55]: Time 3.719613 seconds, bootstrap likelihood -8118.195297, best rearrangement setting 11 Bootstrap[56]: Time 3.361076 seconds, bootstrap likelihood -9239.719110, best rearrangement setting 5 Bootstrap[57]: Time 3.020389 seconds, bootstrap likelihood -8802.510983, best rearrangement setting 7 Bootstrap[58]: Time 3.078280 seconds, bootstrap likelihood -8025.283236, best rearrangement setting 10 Bootstrap[59]: Time 3.407087 seconds, bootstrap likelihood -8551.721193, best rearrangement setting 9 Bootstrap[60]: Time 3.210994 seconds, bootstrap likelihood -8376.851187, best rearrangement setting 7 Bootstrap[61]: Time 3.477800 seconds, bootstrap likelihood -9215.710761, best rearrangement setting 5 Bootstrap[62]: Time 3.162003 seconds, bootstrap likelihood -8281.073446, best rearrangement setting 11 Bootstrap[63]: Time 3.584297 seconds, bootstrap likelihood -8249.887322, best rearrangement setting 12 Bootstrap[64]: Time 3.518607 seconds, bootstrap likelihood -8289.035422, best rearrangement setting 7 Bootstrap[65]: Time 3.319736 seconds, bootstrap likelihood -8292.758556, best rearrangement setting 5 Bootstrap[66]: Time 3.093651 seconds, bootstrap likelihood -8041.425174, best rearrangement setting 5 Bootstrap[67]: Time 3.336752 seconds, bootstrap likelihood -8430.170655, best rearrangement setting 15 Bootstrap[68]: Time 3.456994 seconds, bootstrap likelihood -9000.141194, best rearrangement setting 11 Bootstrap[69]: Time 3.425188 seconds, bootstrap likelihood -9643.864897, best rearrangement setting 5 Bootstrap[70]: Time 3.577212 seconds, bootstrap likelihood -8508.870204, best rearrangement setting 8 Bootstrap[71]: Time 3.466372 seconds, bootstrap likelihood -9242.940274, best rearrangement setting 10 Bootstrap[72]: Time 3.014842 seconds, bootstrap likelihood -8894.585569, best rearrangement setting 11 Bootstrap[73]: Time 3.139956 seconds, bootstrap likelihood -8941.126456, best rearrangement setting 9 Bootstrap[74]: Time 3.227671 seconds, bootstrap likelihood -8928.261489, best rearrangement setting 5 Bootstrap[75]: Time 3.614256 seconds, bootstrap likelihood -8247.418129, best rearrangement setting 8 Bootstrap[76]: Time 4.298844 seconds, bootstrap likelihood -8950.679414, best rearrangement setting 9 Bootstrap[77]: Time 3.634646 seconds, bootstrap likelihood -8246.210780, best rearrangement setting 11 Bootstrap[78]: Time 3.471890 seconds, bootstrap likelihood -8678.725323, best rearrangement setting 15 Bootstrap[79]: Time 4.395325 seconds, bootstrap likelihood -8229.618781, best rearrangement setting 9 Bootstrap[80]: Time 4.111641 seconds, bootstrap likelihood -8150.572740, best rearrangement setting 15 Bootstrap[81]: Time 3.489984 seconds, bootstrap likelihood -9049.932893, best rearrangement setting 7 Bootstrap[82]: Time 3.620583 seconds, bootstrap likelihood -7730.623909, best rearrangement setting 6 Bootstrap[83]: Time 3.407782 seconds, bootstrap likelihood -8619.083476, best rearrangement setting 10 Bootstrap[84]: Time 3.324123 seconds, bootstrap likelihood -7755.895967, best rearrangement setting 11 Bootstrap[85]: Time 3.126142 seconds, bootstrap likelihood -8664.117038, best rearrangement setting 8 Bootstrap[86]: Time 3.589243 seconds, bootstrap likelihood -8229.402911, best rearrangement setting 7 Bootstrap[87]: Time 2.792682 seconds, bootstrap likelihood -7990.466539, best rearrangement setting 7 Bootstrap[88]: Time 3.058433 seconds, bootstrap likelihood -7871.471247, best rearrangement setting 12 Bootstrap[89]: Time 3.092165 seconds, bootstrap likelihood -8542.303187, best rearrangement setting 10 Bootstrap[90]: Time 3.783748 seconds, bootstrap likelihood -9252.210947, best rearrangement setting 8 Bootstrap[91]: Time 3.291246 seconds, bootstrap likelihood -7721.603916, best rearrangement setting 12 Bootstrap[92]: Time 3.616511 seconds, bootstrap likelihood -8610.971426, best rearrangement setting 13 Bootstrap[93]: Time 3.622176 seconds, bootstrap likelihood -7922.572779, best rearrangement setting 15 Bootstrap[94]: Time 3.143624 seconds, bootstrap likelihood -7987.905712, best rearrangement setting 5 Bootstrap[95]: Time 3.550755 seconds, bootstrap likelihood -8382.375006, best rearrangement setting 5 Bootstrap[96]: Time 3.589073 seconds, bootstrap likelihood -9001.049887, best rearrangement setting 13 Bootstrap[97]: Time 3.219688 seconds, bootstrap likelihood -8763.822898, best rearrangement setting 11 Bootstrap[98]: Time 3.524099 seconds, bootstrap likelihood -8611.924116, best rearrangement setting 6 Bootstrap[99]: Time 3.687660 seconds, bootstrap likelihood -8307.568283, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 345.889502 seconds Average Time per Rapid Bootstrap 3.458895 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 298.062211 seconds Slow ML Search 0 Likelihood: -8586.791689 Slow ML Search 1 Likelihood: -8586.791725 Slow ML Search 2 Likelihood: -8586.791725 Slow ML Search 3 Likelihood: -8586.791725 Slow ML Search 4 Likelihood: -8586.791725 Slow ML Search 5 Likelihood: -8586.791725 Slow ML Search 6 Likelihood: -8586.791725 Slow ML Search 7 Likelihood: -8586.791737 Slow ML Search 8 Likelihood: -8586.791738 Slow ML Search 9 Likelihood: -8586.791737 Slow ML optimization finished Slow ML search Time: 122.189744 seconds Thorough ML search Time: 12.392324 seconds Final ML Optimization Likelihood: -8586.794571 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.332149 Tree-Length: 41.118264 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 432.733186 secs or 0.120204 hours Combined Bootstrap and ML search took 778.623497 secs or 0.216284 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.Noctiluca-scintillans-Unknown.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Noctiluca-scintillans-Unknown.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Noctiluca-scintillans-Unknown.MUSCLE All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.Noctiluca-scintillans-Unknown.MUSCLE Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Noctiluca-scintillans-Unknown.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.Noctiluca-scintillans-Unknown.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.Noctiluca-scintillans-Unknown.MUSCLE Overall execution time for full ML analysis: 778.637663 secs or 0.216288 hours or 0.009012 days