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 416 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 74.56% 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: 416 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Karenia-brevis-Wilson.MUSCLE.fa -n Karenia-brevis-Wilson.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.234506 Bootstrap[0]: Time 3.741181 seconds, bootstrap likelihood -9877.532319, best rearrangement setting 13 Bootstrap[1]: Time 3.582106 seconds, bootstrap likelihood -11011.753620, best rearrangement setting 13 Bootstrap[2]: Time 3.253808 seconds, bootstrap likelihood -9851.580048, best rearrangement setting 12 Bootstrap[3]: Time 2.942354 seconds, bootstrap likelihood -10514.137516, best rearrangement setting 15 Bootstrap[4]: Time 2.919158 seconds, bootstrap likelihood -9451.993055, best rearrangement setting 10 Bootstrap[5]: Time 3.198985 seconds, bootstrap likelihood -9389.890678, best rearrangement setting 10 Bootstrap[6]: Time 2.924674 seconds, bootstrap likelihood -9701.916425, best rearrangement setting 6 Bootstrap[7]: Time 3.294149 seconds, bootstrap likelihood -9081.070966, best rearrangement setting 14 Bootstrap[8]: Time 2.889362 seconds, bootstrap likelihood -10535.073458, best rearrangement setting 5 Bootstrap[9]: Time 3.143745 seconds, bootstrap likelihood -9758.224876, best rearrangement setting 7 Bootstrap[10]: Time 2.610831 seconds, bootstrap likelihood -8531.371738, best rearrangement setting 7 Bootstrap[11]: Time 3.159849 seconds, bootstrap likelihood -10165.886027, best rearrangement setting 5 Bootstrap[12]: Time 2.938944 seconds, bootstrap likelihood -10473.856437, best rearrangement setting 8 Bootstrap[13]: Time 2.997518 seconds, bootstrap likelihood -9795.522617, best rearrangement setting 7 Bootstrap[14]: Time 3.705648 seconds, bootstrap likelihood -10005.725211, best rearrangement setting 12 Bootstrap[15]: Time 3.309734 seconds, bootstrap likelihood -9340.976455, best rearrangement setting 15 Bootstrap[16]: Time 3.799370 seconds, bootstrap likelihood -9088.214745, best rearrangement setting 12 Bootstrap[17]: Time 3.245076 seconds, bootstrap likelihood -9742.697813, best rearrangement setting 12 Bootstrap[18]: Time 2.620046 seconds, bootstrap likelihood -9463.353492, best rearrangement setting 5 Bootstrap[19]: Time 3.126686 seconds, bootstrap likelihood -9441.025448, best rearrangement setting 8 Bootstrap[20]: Time 3.438657 seconds, bootstrap likelihood -9145.255383, best rearrangement setting 10 Bootstrap[21]: Time 2.783597 seconds, bootstrap likelihood -10849.711858, best rearrangement setting 6 Bootstrap[22]: Time 3.443447 seconds, bootstrap likelihood -9448.183688, best rearrangement setting 5 Bootstrap[23]: Time 3.027202 seconds, bootstrap likelihood -9276.699835, best rearrangement setting 7 Bootstrap[24]: Time 3.256990 seconds, bootstrap likelihood -9755.398287, best rearrangement setting 8 Bootstrap[25]: Time 3.541573 seconds, bootstrap likelihood -10226.618040, best rearrangement setting 6 Bootstrap[26]: Time 2.688574 seconds, bootstrap likelihood -9169.327091, best rearrangement setting 12 Bootstrap[27]: Time 3.521548 seconds, bootstrap likelihood -9856.398068, best rearrangement setting 10 Bootstrap[28]: Time 3.311759 seconds, bootstrap likelihood -10704.913145, best rearrangement setting 11 Bootstrap[29]: Time 3.139747 seconds, bootstrap likelihood -10379.776504, best rearrangement setting 12 Bootstrap[30]: Time 3.664030 seconds, bootstrap likelihood -9778.145109, best rearrangement setting 15 Bootstrap[31]: Time 3.024228 seconds, bootstrap likelihood -9931.711235, best rearrangement setting 15 Bootstrap[32]: Time 3.355081 seconds, bootstrap likelihood -10617.259432, best rearrangement setting 6 Bootstrap[33]: Time 3.126317 seconds, bootstrap likelihood -9665.551055, best rearrangement setting 15 Bootstrap[34]: Time 3.013211 seconds, bootstrap likelihood -10260.624400, best rearrangement setting 11 Bootstrap[35]: Time 2.892669 seconds, bootstrap likelihood -9479.163794, best rearrangement setting 8 Bootstrap[36]: Time 3.075393 seconds, bootstrap likelihood -9839.314091, best rearrangement setting 9 Bootstrap[37]: Time 3.234370 seconds, bootstrap likelihood -11248.014025, best rearrangement setting 11 Bootstrap[38]: Time 3.424174 seconds, bootstrap likelihood -10194.920970, best rearrangement setting 8 Bootstrap[39]: Time 3.380433 seconds, bootstrap likelihood -9001.665683, best rearrangement setting 13 Bootstrap[40]: Time 4.202790 seconds, bootstrap likelihood -10126.643841, best rearrangement setting 13 Bootstrap[41]: Time 3.509544 seconds, bootstrap likelihood -11854.007072, best rearrangement setting 10 Bootstrap[42]: Time 2.937319 seconds, bootstrap likelihood -9709.971225, best rearrangement setting 5 Bootstrap[43]: Time 3.398831 seconds, bootstrap likelihood -10391.234519, best rearrangement setting 14 Bootstrap[44]: Time 2.846752 seconds, bootstrap likelihood -11249.276975, best rearrangement setting 10 Bootstrap[45]: Time 3.299245 seconds, bootstrap likelihood -8693.209145, best rearrangement setting 15 Bootstrap[46]: Time 3.103898 seconds, bootstrap likelihood -9888.316043, best rearrangement setting 14 Bootstrap[47]: Time 3.028841 seconds, bootstrap likelihood -9864.037335, best rearrangement setting 8 Bootstrap[48]: Time 3.083262 seconds, bootstrap likelihood -10280.258851, best rearrangement setting 6 Bootstrap[49]: Time 3.117063 seconds, bootstrap likelihood -10303.752504, best rearrangement setting 7 Bootstrap[50]: Time 2.884140 seconds, bootstrap likelihood -9275.713035, best rearrangement setting 7 Bootstrap[51]: Time 3.551978 seconds, bootstrap likelihood -9675.748438, best rearrangement setting 11 Bootstrap[52]: Time 3.383644 seconds, bootstrap likelihood -11004.562398, best rearrangement setting 12 Bootstrap[53]: Time 3.290204 seconds, bootstrap likelihood -10313.147991, best rearrangement setting 8 Bootstrap[54]: Time 3.058677 seconds, bootstrap likelihood -9753.423549, best rearrangement setting 9 Bootstrap[55]: Time 2.995440 seconds, bootstrap likelihood -10550.281693, best rearrangement setting 11 Bootstrap[56]: Time 3.433578 seconds, bootstrap likelihood -9709.946872, best rearrangement setting 5 Bootstrap[57]: Time 3.285768 seconds, bootstrap likelihood -10454.781283, best rearrangement setting 7 Bootstrap[58]: Time 3.574363 seconds, bootstrap likelihood -9996.619808, best rearrangement setting 10 Bootstrap[59]: Time 3.367122 seconds, bootstrap likelihood -10141.259101, best rearrangement setting 9 Bootstrap[60]: Time 3.208212 seconds, bootstrap likelihood -9370.694155, best rearrangement setting 7 Bootstrap[61]: Time 3.117241 seconds, bootstrap likelihood -9155.447295, best rearrangement setting 5 Bootstrap[62]: Time 3.090864 seconds, bootstrap likelihood -10627.055174, best rearrangement setting 11 Bootstrap[63]: Time 2.878905 seconds, bootstrap likelihood -10814.184696, best rearrangement setting 12 Bootstrap[64]: Time 3.201480 seconds, bootstrap likelihood -10659.964983, best rearrangement setting 7 Bootstrap[65]: Time 3.545242 seconds, bootstrap likelihood -9975.744124, best rearrangement setting 5 Bootstrap[66]: Time 3.228967 seconds, bootstrap likelihood -10385.567729, best rearrangement setting 5 Bootstrap[67]: Time 3.607201 seconds, bootstrap likelihood -11372.212149, best rearrangement setting 15 Bootstrap[68]: Time 3.815327 seconds, bootstrap likelihood -10253.927316, best rearrangement setting 11 Bootstrap[69]: Time 3.489224 seconds, bootstrap likelihood -9982.967360, best rearrangement setting 5 Bootstrap[70]: Time 2.959153 seconds, bootstrap likelihood -9373.055865, best rearrangement setting 8 Bootstrap[71]: Time 3.065933 seconds, bootstrap likelihood -9820.686849, best rearrangement setting 10 Bootstrap[72]: Time 3.136048 seconds, bootstrap likelihood -9881.016194, best rearrangement setting 11 Bootstrap[73]: Time 2.868383 seconds, bootstrap likelihood -10181.783772, best rearrangement setting 9 Bootstrap[74]: Time 3.496419 seconds, bootstrap likelihood -10159.766485, best rearrangement setting 5 Bootstrap[75]: Time 3.196315 seconds, bootstrap likelihood -10285.637443, best rearrangement setting 8 Bootstrap[76]: Time 3.573141 seconds, bootstrap likelihood -10289.992667, best rearrangement setting 9 Bootstrap[77]: Time 3.938389 seconds, bootstrap likelihood -9750.211223, best rearrangement setting 11 Bootstrap[78]: Time 3.265719 seconds, bootstrap likelihood -9053.743193, best rearrangement setting 15 Bootstrap[79]: Time 3.191294 seconds, bootstrap likelihood -10643.734641, best rearrangement setting 9 Bootstrap[80]: Time 3.146749 seconds, bootstrap likelihood -9643.159523, best rearrangement setting 15 Bootstrap[81]: Time 3.164063 seconds, bootstrap likelihood -9356.956290, best rearrangement setting 7 Bootstrap[82]: Time 3.272741 seconds, bootstrap likelihood -9708.639315, best rearrangement setting 6 Bootstrap[83]: Time 3.048823 seconds, bootstrap likelihood -9991.413958, best rearrangement setting 10 Bootstrap[84]: Time 2.981136 seconds, bootstrap likelihood -9980.912436, best rearrangement setting 11 Bootstrap[85]: Time 3.103853 seconds, bootstrap likelihood -10234.274787, best rearrangement setting 8 Bootstrap[86]: Time 3.125482 seconds, bootstrap likelihood -9323.503475, best rearrangement setting 7 Bootstrap[87]: Time 3.287360 seconds, bootstrap likelihood -9865.660115, best rearrangement setting 7 Bootstrap[88]: Time 4.085778 seconds, bootstrap likelihood -9668.000597, best rearrangement setting 12 Bootstrap[89]: Time 3.368579 seconds, bootstrap likelihood -10652.936467, best rearrangement setting 10 Bootstrap[90]: Time 3.380307 seconds, bootstrap likelihood -10379.547010, best rearrangement setting 8 Bootstrap[91]: Time 3.425108 seconds, bootstrap likelihood -10663.454477, best rearrangement setting 12 Bootstrap[92]: Time 3.204010 seconds, bootstrap likelihood -10946.423058, best rearrangement setting 13 Bootstrap[93]: Time 2.650095 seconds, bootstrap likelihood -9733.927482, best rearrangement setting 15 Bootstrap[94]: Time 2.753703 seconds, bootstrap likelihood -9552.622549, best rearrangement setting 5 Bootstrap[95]: Time 2.735290 seconds, bootstrap likelihood -10425.012335, best rearrangement setting 5 Bootstrap[96]: Time 3.718334 seconds, bootstrap likelihood -9433.352699, best rearrangement setting 13 Bootstrap[97]: Time 3.562803 seconds, bootstrap likelihood -9717.654792, best rearrangement setting 11 Bootstrap[98]: Time 3.670131 seconds, bootstrap likelihood -9761.558027, best rearrangement setting 6 Bootstrap[99]: Time 3.047462 seconds, bootstrap likelihood -10239.978053, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 323.786942 seconds Average Time per Rapid Bootstrap 3.237869 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 297.685243 seconds Slow ML Search 0 Likelihood: -10035.162598 Slow ML Search 1 Likelihood: -10035.162598 Slow ML Search 2 Likelihood: -10035.162598 Slow ML Search 3 Likelihood: -10035.163391 Slow ML Search 4 Likelihood: -10035.166452 Slow ML Search 5 Likelihood: -10035.162649 Slow ML Search 6 Likelihood: -10035.162649 Slow ML Search 7 Likelihood: -10035.162649 Slow ML Search 8 Likelihood: -10035.165119 Slow ML Search 9 Likelihood: -10035.165115 Slow ML optimization finished Slow ML search Time: 137.134810 seconds Thorough ML search Time: 15.384124 seconds Final ML Optimization Likelihood: -10035.162995 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.562116 Tree-Length: 40.957412 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 450.294730 secs or 0.125082 hours Combined Bootstrap and ML search took 774.082466 secs or 0.215023 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-Wilson.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Karenia-brevis-Wilson.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Karenia-brevis-Wilson.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-Wilson.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-Wilson.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-Wilson.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-Wilson.MUSCLE Overall execution time for full ML analysis: 774.097171 secs or 0.215027 hours or 0.008959 days