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 436 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 76.71% 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: 436 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Karenia-brevis-CCMP2229.MUSCLE.fa -n Karenia-brevis-CCMP2229.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.126053 Bootstrap[0]: Time 3.442992 seconds, bootstrap likelihood -9725.926151, best rearrangement setting 13 Bootstrap[1]: Time 3.004837 seconds, bootstrap likelihood -10582.651058, best rearrangement setting 13 Bootstrap[2]: Time 3.208831 seconds, bootstrap likelihood -9409.249322, best rearrangement setting 12 Bootstrap[3]: Time 3.304771 seconds, bootstrap likelihood -9895.426073, best rearrangement setting 15 Bootstrap[4]: Time 3.228755 seconds, bootstrap likelihood -9709.878190, best rearrangement setting 10 Bootstrap[5]: Time 3.177543 seconds, bootstrap likelihood -9856.311228, best rearrangement setting 10 Bootstrap[6]: Time 3.022414 seconds, bootstrap likelihood -9565.035798, best rearrangement setting 6 Bootstrap[7]: Time 3.657996 seconds, bootstrap likelihood -9973.175963, best rearrangement setting 14 Bootstrap[8]: Time 3.329563 seconds, bootstrap likelihood -9632.950328, best rearrangement setting 5 Bootstrap[9]: Time 3.104743 seconds, bootstrap likelihood -9765.925968, best rearrangement setting 7 Bootstrap[10]: Time 3.722682 seconds, bootstrap likelihood -10351.011157, best rearrangement setting 7 Bootstrap[11]: Time 2.944482 seconds, bootstrap likelihood -9925.490650, best rearrangement setting 5 Bootstrap[12]: Time 3.612838 seconds, bootstrap likelihood -9814.810781, best rearrangement setting 8 Bootstrap[13]: Time 3.253512 seconds, bootstrap likelihood -9577.509268, best rearrangement setting 7 Bootstrap[14]: Time 3.448161 seconds, bootstrap likelihood -9703.676601, best rearrangement setting 12 Bootstrap[15]: Time 3.062800 seconds, bootstrap likelihood -9656.231155, best rearrangement setting 15 Bootstrap[16]: Time 3.317582 seconds, bootstrap likelihood -9553.083119, best rearrangement setting 12 Bootstrap[17]: Time 3.128670 seconds, bootstrap likelihood -10040.122422, best rearrangement setting 12 Bootstrap[18]: Time 2.805427 seconds, bootstrap likelihood -9305.116868, best rearrangement setting 5 Bootstrap[19]: Time 3.110023 seconds, bootstrap likelihood -9840.457187, best rearrangement setting 8 Bootstrap[20]: Time 3.539305 seconds, bootstrap likelihood -9252.502565, best rearrangement setting 10 Bootstrap[21]: Time 3.222145 seconds, bootstrap likelihood -9070.834077, best rearrangement setting 6 Bootstrap[22]: Time 3.246997 seconds, bootstrap likelihood -10498.718368, best rearrangement setting 5 Bootstrap[23]: Time 3.712203 seconds, bootstrap likelihood -10167.351123, best rearrangement setting 7 Bootstrap[24]: Time 3.534212 seconds, bootstrap likelihood -9703.079260, best rearrangement setting 8 Bootstrap[25]: Time 3.175552 seconds, bootstrap likelihood -10033.240077, best rearrangement setting 6 Bootstrap[26]: Time 2.807342 seconds, bootstrap likelihood -9315.949645, best rearrangement setting 12 Bootstrap[27]: Time 3.194992 seconds, bootstrap likelihood -9897.307333, best rearrangement setting 10 Bootstrap[28]: Time 3.598980 seconds, bootstrap likelihood -9827.196129, best rearrangement setting 11 Bootstrap[29]: Time 3.014209 seconds, bootstrap likelihood -9752.386192, best rearrangement setting 12 Bootstrap[30]: Time 3.462797 seconds, bootstrap likelihood -9741.127740, best rearrangement setting 15 Bootstrap[31]: Time 3.254294 seconds, bootstrap likelihood -10034.514606, best rearrangement setting 15 Bootstrap[32]: Time 3.351689 seconds, bootstrap likelihood -9490.917412, best rearrangement setting 6 Bootstrap[33]: Time 3.062655 seconds, bootstrap likelihood -10167.252969, best rearrangement setting 15 Bootstrap[34]: Time 3.555928 seconds, bootstrap likelihood -10151.576313, best rearrangement setting 11 Bootstrap[35]: Time 3.582987 seconds, bootstrap likelihood -9778.431803, best rearrangement setting 8 Bootstrap[36]: Time 3.610644 seconds, bootstrap likelihood -10501.250815, best rearrangement setting 9 Bootstrap[37]: Time 3.088826 seconds, bootstrap likelihood -10700.304369, best rearrangement setting 11 Bootstrap[38]: Time 3.607101 seconds, bootstrap likelihood -9380.751938, best rearrangement setting 8 Bootstrap[39]: Time 3.036432 seconds, bootstrap likelihood -9918.680191, best rearrangement setting 13 Bootstrap[40]: Time 2.896750 seconds, bootstrap likelihood -10082.699192, best rearrangement setting 13 Bootstrap[41]: Time 3.565694 seconds, bootstrap likelihood -9265.297960, best rearrangement setting 10 Bootstrap[42]: Time 3.624113 seconds, bootstrap likelihood -10770.117634, best rearrangement setting 5 Bootstrap[43]: Time 3.324437 seconds, bootstrap likelihood -10145.403425, best rearrangement setting 14 Bootstrap[44]: Time 3.065498 seconds, bootstrap likelihood -9526.143457, best rearrangement setting 10 Bootstrap[45]: Time 3.179140 seconds, bootstrap likelihood -9724.326351, best rearrangement setting 15 Bootstrap[46]: Time 3.290684 seconds, bootstrap likelihood -9464.984574, best rearrangement setting 14 Bootstrap[47]: Time 3.575298 seconds, bootstrap likelihood -9870.535275, best rearrangement setting 8 Bootstrap[48]: Time 2.779581 seconds, bootstrap likelihood -8707.071914, best rearrangement setting 6 Bootstrap[49]: Time 3.334514 seconds, bootstrap likelihood -10411.234516, best rearrangement setting 7 Bootstrap[50]: Time 3.326565 seconds, bootstrap likelihood -10007.359897, best rearrangement setting 7 Bootstrap[51]: Time 3.262989 seconds, bootstrap likelihood -9677.104890, best rearrangement setting 11 Bootstrap[52]: Time 2.560898 seconds, bootstrap likelihood -9393.924851, best rearrangement setting 12 Bootstrap[53]: Time 3.249400 seconds, bootstrap likelihood -9378.842987, best rearrangement setting 8 Bootstrap[54]: Time 3.245106 seconds, bootstrap likelihood -9739.289000, best rearrangement setting 9 Bootstrap[55]: Time 2.775113 seconds, bootstrap likelihood -9569.718943, best rearrangement setting 11 Bootstrap[56]: Time 2.986656 seconds, bootstrap likelihood -10531.604118, best rearrangement setting 5 Bootstrap[57]: Time 2.977776 seconds, bootstrap likelihood -10750.115732, best rearrangement setting 7 Bootstrap[58]: Time 3.304062 seconds, bootstrap likelihood -10602.860540, best rearrangement setting 10 Bootstrap[59]: Time 2.969028 seconds, bootstrap likelihood -10587.782186, best rearrangement setting 9 Bootstrap[60]: Time 3.627673 seconds, bootstrap likelihood -10227.461398, best rearrangement setting 7 Bootstrap[61]: Time 2.900426 seconds, bootstrap likelihood -10116.252792, best rearrangement setting 5 Bootstrap[62]: Time 3.745419 seconds, bootstrap likelihood -9247.710324, best rearrangement setting 11 Bootstrap[63]: Time 3.368865 seconds, bootstrap likelihood -8904.500039, best rearrangement setting 12 Bootstrap[64]: Time 4.232679 seconds, bootstrap likelihood -10302.596655, best rearrangement setting 7 Bootstrap[65]: Time 3.524980 seconds, bootstrap likelihood -9943.940793, best rearrangement setting 5 Bootstrap[66]: Time 3.048819 seconds, bootstrap likelihood -9105.211759, best rearrangement setting 5 Bootstrap[67]: Time 3.252634 seconds, bootstrap likelihood -10305.340252, best rearrangement setting 15 Bootstrap[68]: Time 3.275504 seconds, bootstrap likelihood -10364.842452, best rearrangement setting 11 Bootstrap[69]: Time 3.537080 seconds, bootstrap likelihood -9571.190691, best rearrangement setting 5 Bootstrap[70]: Time 3.431489 seconds, bootstrap likelihood -9140.447311, best rearrangement setting 8 Bootstrap[71]: Time 3.543980 seconds, bootstrap likelihood -9803.301638, best rearrangement setting 10 Bootstrap[72]: Time 3.360273 seconds, bootstrap likelihood -9618.093696, best rearrangement setting 11 Bootstrap[73]: Time 3.448759 seconds, bootstrap likelihood -8782.778683, best rearrangement setting 9 Bootstrap[74]: Time 2.794502 seconds, bootstrap likelihood -8842.679880, best rearrangement setting 5 Bootstrap[75]: Time 3.539190 seconds, bootstrap likelihood -10592.228656, best rearrangement setting 8 Bootstrap[76]: Time 3.763148 seconds, bootstrap likelihood -9529.795782, best rearrangement setting 9 Bootstrap[77]: Time 3.430072 seconds, bootstrap likelihood -8894.187213, best rearrangement setting 11 Bootstrap[78]: Time 2.728649 seconds, bootstrap likelihood -9146.291587, best rearrangement setting 15 Bootstrap[79]: Time 3.154009 seconds, bootstrap likelihood -10193.299657, best rearrangement setting 9 Bootstrap[80]: Time 3.195820 seconds, bootstrap likelihood -10372.482458, best rearrangement setting 15 Bootstrap[81]: Time 2.944521 seconds, bootstrap likelihood -10169.686168, best rearrangement setting 7 Bootstrap[82]: Time 3.838326 seconds, bootstrap likelihood -9658.938220, best rearrangement setting 6 Bootstrap[83]: Time 3.198861 seconds, bootstrap likelihood -9073.672484, best rearrangement setting 10 Bootstrap[84]: Time 3.373653 seconds, bootstrap likelihood -10069.334772, best rearrangement setting 11 Bootstrap[85]: Time 3.042159 seconds, bootstrap likelihood -10498.864134, best rearrangement setting 8 Bootstrap[86]: Time 3.355370 seconds, bootstrap likelihood -9453.320673, best rearrangement setting 7 Bootstrap[87]: Time 3.487146 seconds, bootstrap likelihood -9840.451457, best rearrangement setting 7 Bootstrap[88]: Time 3.474893 seconds, bootstrap likelihood -10601.855639, best rearrangement setting 12 Bootstrap[89]: Time 3.145822 seconds, bootstrap likelihood -9376.745418, best rearrangement setting 10 Bootstrap[90]: Time 3.167014 seconds, bootstrap likelihood -9268.600929, best rearrangement setting 8 Bootstrap[91]: Time 3.370889 seconds, bootstrap likelihood -9965.454741, best rearrangement setting 12 Bootstrap[92]: Time 3.655688 seconds, bootstrap likelihood -10298.163489, best rearrangement setting 13 Bootstrap[93]: Time 3.453825 seconds, bootstrap likelihood -9802.153113, best rearrangement setting 15 Bootstrap[94]: Time 3.140463 seconds, bootstrap likelihood -9651.082914, best rearrangement setting 5 Bootstrap[95]: Time 3.045198 seconds, bootstrap likelihood -9160.539683, best rearrangement setting 5 Bootstrap[96]: Time 3.387347 seconds, bootstrap likelihood -9680.433000, best rearrangement setting 13 Bootstrap[97]: Time 3.395180 seconds, bootstrap likelihood -9857.000156, best rearrangement setting 11 Bootstrap[98]: Time 2.692940 seconds, bootstrap likelihood -9699.360742, best rearrangement setting 6 Bootstrap[99]: Time 3.398990 seconds, bootstrap likelihood -9790.956775, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 328.401769 seconds Average Time per Rapid Bootstrap 3.284018 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 391.440935 seconds Slow ML Search 0 Likelihood: -9809.800006 Slow ML Search 1 Likelihood: -9809.800006 Slow ML Search 2 Likelihood: -9809.800006 Slow ML Search 3 Likelihood: -9809.800006 Slow ML Search 4 Likelihood: -9809.800055 Slow ML Search 5 Likelihood: -9809.800055 Slow ML Search 6 Likelihood: -9809.800055 Slow ML Search 7 Likelihood: -9809.800055 Slow ML Search 8 Likelihood: -9809.800055 Slow ML Search 9 Likelihood: -9809.800055 Slow ML optimization finished Slow ML search Time: 118.867963 seconds Thorough ML search Time: 15.935989 seconds Final ML Optimization Likelihood: -9809.800428 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.470630 Tree-Length: 39.294844 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 526.334464 secs or 0.146204 hours Combined Bootstrap and ML search took 854.737080 secs or 0.237427 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.Karenia-brevis-CCMP2229.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Karenia-brevis-CCMP2229.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Karenia-brevis-CCMP2229.MUSCLE All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.Karenia-brevis-CCMP2229.MUSCLE Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Karenia-brevis-CCMP2229.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.Karenia-brevis-CCMP2229.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.Karenia-brevis-CCMP2229.MUSCLE Overall execution time for full ML analysis: 854.751660 secs or 0.237431 hours or 0.009893 days