IMPORTANT WARNING: Alignment column 181 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 1 column that contains only undetermined values which will be treated as missing data. Normally these columns should be excluded from the analysis. Just in case you might need it, an alignment file with undetermined columns removed is printed to file Azadinium-spinosum-3D9.MUSCLE.fa.reduced 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 467 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 71.86% 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: 467 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Azadinium-spinosum-3D9.MUSCLE.fa -n Azadinium-spinosum-3D9.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.098666 Bootstrap[0]: Time 4.063164 seconds, bootstrap likelihood -9157.585169, best rearrangement setting 13 Bootstrap[1]: Time 3.306852 seconds, bootstrap likelihood -9141.522089, best rearrangement setting 13 Bootstrap[2]: Time 3.380675 seconds, bootstrap likelihood -9045.451638, best rearrangement setting 12 Bootstrap[3]: Time 3.427150 seconds, bootstrap likelihood -8520.725260, best rearrangement setting 15 Bootstrap[4]: Time 3.120676 seconds, bootstrap likelihood -8764.487551, best rearrangement setting 10 Bootstrap[5]: Time 3.511422 seconds, bootstrap likelihood -8977.938317, best rearrangement setting 10 Bootstrap[6]: Time 2.854651 seconds, bootstrap likelihood -9023.884117, best rearrangement setting 6 Bootstrap[7]: Time 3.356450 seconds, bootstrap likelihood -8815.504116, best rearrangement setting 14 Bootstrap[8]: Time 3.366558 seconds, bootstrap likelihood -8972.255657, best rearrangement setting 5 Bootstrap[9]: Time 3.337834 seconds, bootstrap likelihood -8564.538196, best rearrangement setting 7 Bootstrap[10]: Time 3.042713 seconds, bootstrap likelihood -8769.853774, best rearrangement setting 7 Bootstrap[11]: Time 3.281906 seconds, bootstrap likelihood -8719.257793, best rearrangement setting 5 Bootstrap[12]: Time 3.151811 seconds, bootstrap likelihood -9419.164109, best rearrangement setting 8 Bootstrap[13]: Time 3.636976 seconds, bootstrap likelihood -9174.015069, best rearrangement setting 7 Bootstrap[14]: Time 3.281655 seconds, bootstrap likelihood -8610.139935, best rearrangement setting 12 Bootstrap[15]: Time 3.431336 seconds, bootstrap likelihood -9306.896800, best rearrangement setting 15 Bootstrap[16]: Time 3.073982 seconds, bootstrap likelihood -8504.881306, best rearrangement setting 12 Bootstrap[17]: Time 3.188442 seconds, bootstrap likelihood -8710.465086, best rearrangement setting 12 Bootstrap[18]: Time 2.846677 seconds, bootstrap likelihood -8868.465675, best rearrangement setting 5 Bootstrap[19]: Time 3.465901 seconds, bootstrap likelihood -8385.422512, best rearrangement setting 8 Bootstrap[20]: Time 2.976384 seconds, bootstrap likelihood -8980.822315, best rearrangement setting 10 Bootstrap[21]: Time 3.184545 seconds, bootstrap likelihood -9508.963346, best rearrangement setting 6 Bootstrap[22]: Time 2.847480 seconds, bootstrap likelihood -8852.156109, best rearrangement setting 5 Bootstrap[23]: Time 2.708285 seconds, bootstrap likelihood -9295.338205, best rearrangement setting 7 Bootstrap[24]: Time 3.092806 seconds, bootstrap likelihood -9283.554500, best rearrangement setting 8 Bootstrap[25]: Time 3.321049 seconds, bootstrap likelihood -8087.459990, best rearrangement setting 6 Bootstrap[26]: Time 3.676369 seconds, bootstrap likelihood -8762.503119, best rearrangement setting 12 Bootstrap[27]: Time 3.963928 seconds, bootstrap likelihood -9673.357663, best rearrangement setting 10 Bootstrap[28]: Time 3.418030 seconds, bootstrap likelihood -8718.203801, best rearrangement setting 11 Bootstrap[29]: Time 3.310505 seconds, bootstrap likelihood -8576.066320, best rearrangement setting 12 Bootstrap[30]: Time 2.962582 seconds, bootstrap likelihood -8399.942854, best rearrangement setting 15 Bootstrap[31]: Time 3.353415 seconds, bootstrap likelihood -8866.919110, best rearrangement setting 15 Bootstrap[32]: Time 3.423180 seconds, bootstrap likelihood -8734.126812, best rearrangement setting 6 Bootstrap[33]: Time 2.861794 seconds, bootstrap likelihood -9739.967713, best rearrangement setting 15 Bootstrap[34]: Time 2.706351 seconds, bootstrap likelihood -8921.766178, best rearrangement setting 11 Bootstrap[35]: Time 3.203189 seconds, bootstrap likelihood -8733.921053, best rearrangement setting 8 Bootstrap[36]: Time 3.346646 seconds, bootstrap likelihood -9058.491458, best rearrangement setting 9 Bootstrap[37]: Time 3.609335 seconds, bootstrap likelihood -9114.225248, best rearrangement setting 11 Bootstrap[38]: Time 3.195717 seconds, bootstrap likelihood -8481.899190, best rearrangement setting 8 Bootstrap[39]: Time 3.598072 seconds, bootstrap likelihood -9452.747844, best rearrangement setting 13 Bootstrap[40]: Time 3.293373 seconds, bootstrap likelihood -9669.556229, best rearrangement setting 13 Bootstrap[41]: Time 2.912075 seconds, bootstrap likelihood -8968.659072, best rearrangement setting 10 Bootstrap[42]: Time 3.334827 seconds, bootstrap likelihood -9481.717758, best rearrangement setting 5 Bootstrap[43]: Time 3.281501 seconds, bootstrap likelihood -9225.435544, best rearrangement setting 14 Bootstrap[44]: Time 3.388562 seconds, bootstrap likelihood -9895.455116, best rearrangement setting 10 Bootstrap[45]: Time 3.175248 seconds, bootstrap likelihood -8358.400954, best rearrangement setting 15 Bootstrap[46]: Time 2.934450 seconds, bootstrap likelihood -9248.472596, best rearrangement setting 14 Bootstrap[47]: Time 3.182777 seconds, bootstrap likelihood -9000.695080, best rearrangement setting 8 Bootstrap[48]: Time 3.373391 seconds, bootstrap likelihood -8973.148612, best rearrangement setting 6 Bootstrap[49]: Time 3.433107 seconds, bootstrap likelihood -8136.544602, best rearrangement setting 7 Bootstrap[50]: Time 3.397661 seconds, bootstrap likelihood -9541.085501, best rearrangement setting 7 Bootstrap[51]: Time 3.138740 seconds, bootstrap likelihood -8682.051174, best rearrangement setting 11 Bootstrap[52]: Time 3.215831 seconds, bootstrap likelihood -9718.538862, best rearrangement setting 12 Bootstrap[53]: Time 3.136017 seconds, bootstrap likelihood -8597.237483, best rearrangement setting 8 Bootstrap[54]: Time 3.071842 seconds, bootstrap likelihood -9143.620416, best rearrangement setting 9 Bootstrap[55]: Time 3.088369 seconds, bootstrap likelihood -8515.717174, best rearrangement setting 11 Bootstrap[56]: Time 2.898575 seconds, bootstrap likelihood -9134.116582, best rearrangement setting 5 Bootstrap[57]: Time 3.750551 seconds, bootstrap likelihood -8841.254352, best rearrangement setting 7 Bootstrap[58]: Time 3.678371 seconds, bootstrap likelihood -9004.737728, best rearrangement setting 10 Bootstrap[59]: Time 2.887838 seconds, bootstrap likelihood -9367.964169, best rearrangement setting 9 Bootstrap[60]: Time 2.646757 seconds, bootstrap likelihood -8625.419946, best rearrangement setting 7 Bootstrap[61]: Time 3.255499 seconds, bootstrap likelihood -9502.243865, best rearrangement setting 5 Bootstrap[62]: Time 3.476435 seconds, bootstrap likelihood -8658.267518, best rearrangement setting 11 Bootstrap[63]: Time 3.392055 seconds, bootstrap likelihood -9010.242792, best rearrangement setting 12 Bootstrap[64]: Time 3.124979 seconds, bootstrap likelihood -8565.040680, best rearrangement setting 7 Bootstrap[65]: Time 3.416354 seconds, bootstrap likelihood -8770.362013, best rearrangement setting 5 Bootstrap[66]: Time 3.155961 seconds, bootstrap likelihood -8008.337383, best rearrangement setting 5 Bootstrap[67]: Time 3.441534 seconds, bootstrap likelihood -9753.447139, best rearrangement setting 15 Bootstrap[68]: Time 3.548549 seconds, bootstrap likelihood -9638.713628, best rearrangement setting 11 Bootstrap[69]: Time 3.336368 seconds, bootstrap likelihood -9349.492551, best rearrangement setting 5 Bootstrap[70]: Time 2.885904 seconds, bootstrap likelihood -9662.164150, best rearrangement setting 8 Bootstrap[71]: Time 3.420514 seconds, bootstrap likelihood -9115.345228, best rearrangement setting 10 Bootstrap[72]: Time 4.137034 seconds, bootstrap likelihood -9058.272170, best rearrangement setting 11 Bootstrap[73]: Time 3.661046 seconds, bootstrap likelihood -9431.014087, best rearrangement setting 9 Bootstrap[74]: Time 3.684883 seconds, bootstrap likelihood -8826.920236, best rearrangement setting 5 Bootstrap[75]: Time 3.039537 seconds, bootstrap likelihood -8412.564654, best rearrangement setting 8 Bootstrap[76]: Time 3.351644 seconds, bootstrap likelihood -9555.171992, best rearrangement setting 9 Bootstrap[77]: Time 3.552227 seconds, bootstrap likelihood -8398.309239, best rearrangement setting 11 Bootstrap[78]: Time 3.573946 seconds, bootstrap likelihood -9347.283647, best rearrangement setting 15 Bootstrap[79]: Time 3.418746 seconds, bootstrap likelihood -8251.401959, best rearrangement setting 9 Bootstrap[80]: Time 3.040390 seconds, bootstrap likelihood -9965.857955, best rearrangement setting 15 Bootstrap[81]: Time 2.907096 seconds, bootstrap likelihood -9360.361146, best rearrangement setting 7 Bootstrap[82]: Time 2.750754 seconds, bootstrap likelihood -8762.497278, best rearrangement setting 6 Bootstrap[83]: Time 2.809242 seconds, bootstrap likelihood -8820.105749, best rearrangement setting 10 Bootstrap[84]: Time 3.323762 seconds, bootstrap likelihood -8519.644388, best rearrangement setting 11 Bootstrap[85]: Time 3.670239 seconds, bootstrap likelihood -8839.900665, best rearrangement setting 8 Bootstrap[86]: Time 3.462978 seconds, bootstrap likelihood -8983.078944, best rearrangement setting 7 Bootstrap[87]: Time 3.364411 seconds, bootstrap likelihood -8332.380758, best rearrangement setting 7 Bootstrap[88]: Time 3.709905 seconds, bootstrap likelihood -8667.740103, best rearrangement setting 12 Bootstrap[89]: Time 2.926083 seconds, bootstrap likelihood -8522.331679, best rearrangement setting 10 Bootstrap[90]: Time 3.698007 seconds, bootstrap likelihood -9115.958896, best rearrangement setting 8 Bootstrap[91]: Time 3.523300 seconds, bootstrap likelihood -8624.420350, best rearrangement setting 12 Bootstrap[92]: Time 3.377086 seconds, bootstrap likelihood -7855.162386, best rearrangement setting 13 Bootstrap[93]: Time 3.128089 seconds, bootstrap likelihood -8451.341836, best rearrangement setting 15 Bootstrap[94]: Time 2.912974 seconds, bootstrap likelihood -8709.193012, best rearrangement setting 5 Bootstrap[95]: Time 3.877530 seconds, bootstrap likelihood -9136.568993, best rearrangement setting 5 Bootstrap[96]: Time 3.227236 seconds, bootstrap likelihood -9149.604998, best rearrangement setting 13 Bootstrap[97]: Time 3.414738 seconds, bootstrap likelihood -9333.708367, best rearrangement setting 11 Bootstrap[98]: Time 3.544159 seconds, bootstrap likelihood -8920.510280, best rearrangement setting 6 Bootstrap[99]: Time 3.082922 seconds, bootstrap likelihood -8809.963695, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 328.820640 seconds Average Time per Rapid Bootstrap 3.288206 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 313.815292 seconds Slow ML Search 0 Likelihood: -8988.872010 Slow ML Search 1 Likelihood: -8988.872011 Slow ML Search 2 Likelihood: -8988.872011 Slow ML Search 3 Likelihood: -8988.872011 Slow ML Search 4 Likelihood: -8988.872012 Slow ML Search 5 Likelihood: -8988.872012 Slow ML Search 6 Likelihood: -8988.872089 Slow ML Search 7 Likelihood: -8988.915390 Slow ML Search 8 Likelihood: -8988.915480 Slow ML Search 9 Likelihood: -8989.448578 Slow ML optimization finished Slow ML search Time: 97.571302 seconds Thorough ML search Time: 13.696552 seconds Final ML Optimization Likelihood: -8988.872474 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.321997 Tree-Length: 36.830007 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 425.170399 secs or 0.118103 hours Combined Bootstrap and ML search took 753.991839 secs or 0.209442 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.Azadinium-spinosum-3D9.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Azadinium-spinosum-3D9.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Azadinium-spinosum-3D9.MUSCLE All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.Azadinium-spinosum-3D9.MUSCLE Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Azadinium-spinosum-3D9.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.Azadinium-spinosum-3D9.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.Azadinium-spinosum-3D9.MUSCLE Overall execution time for full ML analysis: 754.006921 secs or 0.209446 hours or 0.008727 days