IMPORTANT WARNING: Alignment column 209 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 Gymnodinium-catenatum-GC744.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 299 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 72.11% 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: 299 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Gymnodinium-catenatum-GC744.MUSCLE.fa -n Gymnodinium-catenatum-GC744.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.181619 Bootstrap[0]: Time 2.753709 seconds, bootstrap likelihood -7208.453428, best rearrangement setting 13 Bootstrap[1]: Time 2.364533 seconds, bootstrap likelihood -6792.103450, best rearrangement setting 13 Bootstrap[2]: Time 2.297159 seconds, bootstrap likelihood -7558.572674, best rearrangement setting 12 Bootstrap[3]: Time 2.503011 seconds, bootstrap likelihood -6752.147948, best rearrangement setting 15 Bootstrap[4]: Time 2.379071 seconds, bootstrap likelihood -6826.846522, best rearrangement setting 10 Bootstrap[5]: Time 2.476285 seconds, bootstrap likelihood -7518.403735, best rearrangement setting 10 Bootstrap[6]: Time 2.717566 seconds, bootstrap likelihood -6786.745101, best rearrangement setting 6 Bootstrap[7]: Time 2.317415 seconds, bootstrap likelihood -6963.402588, best rearrangement setting 14 Bootstrap[8]: Time 2.214372 seconds, bootstrap likelihood -6744.740074, best rearrangement setting 5 Bootstrap[9]: Time 2.192715 seconds, bootstrap likelihood -6899.024909, best rearrangement setting 7 Bootstrap[10]: Time 2.028526 seconds, bootstrap likelihood -6873.834617, best rearrangement setting 7 Bootstrap[11]: Time 2.112268 seconds, bootstrap likelihood -6731.035270, best rearrangement setting 5 Bootstrap[12]: Time 2.248775 seconds, bootstrap likelihood -6647.935054, best rearrangement setting 8 Bootstrap[13]: Time 2.204766 seconds, bootstrap likelihood -6953.568514, best rearrangement setting 7 Bootstrap[14]: Time 2.040353 seconds, bootstrap likelihood -7277.364410, best rearrangement setting 12 Bootstrap[15]: Time 2.381330 seconds, bootstrap likelihood -6358.833831, best rearrangement setting 15 Bootstrap[16]: Time 2.131179 seconds, bootstrap likelihood -6884.750097, best rearrangement setting 12 Bootstrap[17]: Time 2.007038 seconds, bootstrap likelihood -6454.997308, best rearrangement setting 12 Bootstrap[18]: Time 2.364723 seconds, bootstrap likelihood -7212.168256, best rearrangement setting 5 Bootstrap[19]: Time 2.270801 seconds, bootstrap likelihood -6720.117979, best rearrangement setting 8 Bootstrap[20]: Time 2.482455 seconds, bootstrap likelihood -7240.735868, best rearrangement setting 10 Bootstrap[21]: Time 2.297793 seconds, bootstrap likelihood -6546.794583, best rearrangement setting 6 Bootstrap[22]: Time 2.075060 seconds, bootstrap likelihood -6518.516890, best rearrangement setting 5 Bootstrap[23]: Time 2.756106 seconds, bootstrap likelihood -7292.533709, best rearrangement setting 7 Bootstrap[24]: Time 2.072686 seconds, bootstrap likelihood -7249.396326, best rearrangement setting 8 Bootstrap[25]: Time 2.155708 seconds, bootstrap likelihood -6597.538636, best rearrangement setting 6 Bootstrap[26]: Time 2.183750 seconds, bootstrap likelihood -6607.700794, best rearrangement setting 12 Bootstrap[27]: Time 2.169946 seconds, bootstrap likelihood -6549.912581, best rearrangement setting 10 Bootstrap[28]: Time 2.242880 seconds, bootstrap likelihood -6864.706395, best rearrangement setting 11 Bootstrap[29]: Time 2.082887 seconds, bootstrap likelihood -7679.512139, best rearrangement setting 12 Bootstrap[30]: Time 2.175279 seconds, bootstrap likelihood -6908.918069, best rearrangement setting 15 Bootstrap[31]: Time 2.233282 seconds, bootstrap likelihood -6263.395253, best rearrangement setting 15 Bootstrap[32]: Time 2.616462 seconds, bootstrap likelihood -6695.409270, best rearrangement setting 6 Bootstrap[33]: Time 2.056631 seconds, bootstrap likelihood -6765.264509, best rearrangement setting 15 Bootstrap[34]: Time 2.016234 seconds, bootstrap likelihood -6804.014137, best rearrangement setting 11 Bootstrap[35]: Time 2.426820 seconds, bootstrap likelihood -6579.423352, best rearrangement setting 8 Bootstrap[36]: Time 2.359347 seconds, bootstrap likelihood -7043.588471, best rearrangement setting 9 Bootstrap[37]: Time 2.136800 seconds, bootstrap likelihood -7125.792326, best rearrangement setting 11 Bootstrap[38]: Time 2.033377 seconds, bootstrap likelihood -6928.363648, best rearrangement setting 8 Bootstrap[39]: Time 2.380029 seconds, bootstrap likelihood -6725.888021, best rearrangement setting 13 Bootstrap[40]: Time 2.446374 seconds, bootstrap likelihood -7015.775751, best rearrangement setting 13 Bootstrap[41]: Time 2.276762 seconds, bootstrap likelihood -6617.187219, best rearrangement setting 10 Bootstrap[42]: Time 2.554808 seconds, bootstrap likelihood -6669.957173, best rearrangement setting 5 Bootstrap[43]: Time 2.409656 seconds, bootstrap likelihood -7798.795939, best rearrangement setting 14 Bootstrap[44]: Time 2.379451 seconds, bootstrap likelihood -7425.152864, best rearrangement setting 10 Bootstrap[45]: Time 2.243134 seconds, bootstrap likelihood -6468.635211, best rearrangement setting 15 Bootstrap[46]: Time 2.012228 seconds, bootstrap likelihood -6798.415162, best rearrangement setting 14 Bootstrap[47]: Time 2.306412 seconds, bootstrap likelihood -7676.715407, best rearrangement setting 8 Bootstrap[48]: Time 2.564766 seconds, bootstrap likelihood -7582.909814, best rearrangement setting 6 Bootstrap[49]: Time 2.092412 seconds, bootstrap likelihood -6118.926434, best rearrangement setting 7 Bootstrap[50]: Time 2.480661 seconds, bootstrap likelihood -6766.279472, best rearrangement setting 7 Bootstrap[51]: Time 2.211662 seconds, bootstrap likelihood -7229.060714, best rearrangement setting 11 Bootstrap[52]: Time 2.677521 seconds, bootstrap likelihood -7157.723280, best rearrangement setting 12 Bootstrap[53]: Time 2.466169 seconds, bootstrap likelihood -6321.161273, best rearrangement setting 8 Bootstrap[54]: Time 2.488367 seconds, bootstrap likelihood -6734.928440, best rearrangement setting 9 Bootstrap[55]: Time 2.354738 seconds, bootstrap likelihood -7213.175904, best rearrangement setting 11 Bootstrap[56]: Time 2.000330 seconds, bootstrap likelihood -7030.364647, best rearrangement setting 5 Bootstrap[57]: Time 2.210115 seconds, bootstrap likelihood -7151.183017, best rearrangement setting 7 Bootstrap[58]: Time 2.506347 seconds, bootstrap likelihood -6899.675748, best rearrangement setting 10 Bootstrap[59]: Time 2.034783 seconds, bootstrap likelihood -6787.855456, best rearrangement setting 9 Bootstrap[60]: Time 2.129020 seconds, bootstrap likelihood -6762.031032, best rearrangement setting 7 Bootstrap[61]: Time 2.152391 seconds, bootstrap likelihood -7173.701785, best rearrangement setting 5 Bootstrap[62]: Time 2.223665 seconds, bootstrap likelihood -6558.246351, best rearrangement setting 11 Bootstrap[63]: Time 2.144523 seconds, bootstrap likelihood -6549.054320, best rearrangement setting 12 Bootstrap[64]: Time 2.620023 seconds, bootstrap likelihood -7559.670228, best rearrangement setting 7 Bootstrap[65]: Time 1.890753 seconds, bootstrap likelihood -6955.941267, best rearrangement setting 5 Bootstrap[66]: Time 2.155613 seconds, bootstrap likelihood -6556.005328, best rearrangement setting 5 Bootstrap[67]: Time 2.318212 seconds, bootstrap likelihood -6877.099343, best rearrangement setting 15 Bootstrap[68]: Time 2.240007 seconds, bootstrap likelihood -6408.222044, best rearrangement setting 11 Bootstrap[69]: Time 2.234465 seconds, bootstrap likelihood -7169.294565, best rearrangement setting 5 Bootstrap[70]: Time 2.248176 seconds, bootstrap likelihood -6771.158606, best rearrangement setting 8 Bootstrap[71]: Time 2.148717 seconds, bootstrap likelihood -6769.457947, best rearrangement setting 10 Bootstrap[72]: Time 2.002422 seconds, bootstrap likelihood -6876.151323, best rearrangement setting 11 Bootstrap[73]: Time 2.255176 seconds, bootstrap likelihood -7229.401160, best rearrangement setting 9 Bootstrap[74]: Time 1.791368 seconds, bootstrap likelihood -7422.881258, best rearrangement setting 5 Bootstrap[75]: Time 2.131629 seconds, bootstrap likelihood -6817.426409, best rearrangement setting 8 Bootstrap[76]: Time 1.898755 seconds, bootstrap likelihood -7257.969223, best rearrangement setting 9 Bootstrap[77]: Time 2.671532 seconds, bootstrap likelihood -7300.339723, best rearrangement setting 11 Bootstrap[78]: Time 1.992467 seconds, bootstrap likelihood -6919.730570, best rearrangement setting 15 Bootstrap[79]: Time 2.238690 seconds, bootstrap likelihood -7125.662066, best rearrangement setting 9 Bootstrap[80]: Time 2.147386 seconds, bootstrap likelihood -6671.821323, best rearrangement setting 15 Bootstrap[81]: Time 2.232749 seconds, bootstrap likelihood -6818.778275, best rearrangement setting 7 Bootstrap[82]: Time 2.021642 seconds, bootstrap likelihood -6348.252572, best rearrangement setting 6 Bootstrap[83]: Time 2.392795 seconds, bootstrap likelihood -7213.625919, best rearrangement setting 10 Bootstrap[84]: Time 1.877132 seconds, bootstrap likelihood -6651.225092, best rearrangement setting 11 Bootstrap[85]: Time 2.279844 seconds, bootstrap likelihood -6567.289208, best rearrangement setting 8 Bootstrap[86]: Time 2.017182 seconds, bootstrap likelihood -6643.594401, best rearrangement setting 7 Bootstrap[87]: Time 2.051860 seconds, bootstrap likelihood -7332.643039, best rearrangement setting 7 Bootstrap[88]: Time 2.223076 seconds, bootstrap likelihood -7301.197832, best rearrangement setting 12 Bootstrap[89]: Time 1.932461 seconds, bootstrap likelihood -6989.720428, best rearrangement setting 10 Bootstrap[90]: Time 2.541181 seconds, bootstrap likelihood -7245.198790, best rearrangement setting 8 Bootstrap[91]: Time 2.375792 seconds, bootstrap likelihood -5915.563499, best rearrangement setting 12 Bootstrap[92]: Time 2.623424 seconds, bootstrap likelihood -6372.605084, best rearrangement setting 13 Bootstrap[93]: Time 2.311250 seconds, bootstrap likelihood -7208.051055, best rearrangement setting 15 Bootstrap[94]: Time 2.296130 seconds, bootstrap likelihood -6738.250207, best rearrangement setting 5 Bootstrap[95]: Time 2.259185 seconds, bootstrap likelihood -6211.703623, best rearrangement setting 5 Bootstrap[96]: Time 2.202835 seconds, bootstrap likelihood -6469.040396, best rearrangement setting 13 Bootstrap[97]: Time 2.454285 seconds, bootstrap likelihood -7462.997069, best rearrangement setting 11 Bootstrap[98]: Time 2.176410 seconds, bootstrap likelihood -7478.989288, best rearrangement setting 6 Bootstrap[99]: Time 2.201321 seconds, bootstrap likelihood -6822.718993, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 225.856609 seconds Average Time per Rapid Bootstrap 2.258566 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 176.932083 seconds Slow ML Search 0 Likelihood: -6914.764209 Slow ML Search 1 Likelihood: -6914.764209 Slow ML Search 2 Likelihood: -6914.764209 Slow ML Search 3 Likelihood: -6914.764209 Slow ML Search 4 Likelihood: -6914.764209 Slow ML Search 5 Likelihood: -6914.764209 Slow ML Search 6 Likelihood: -6914.764209 Slow ML Search 7 Likelihood: -6914.764209 Slow ML Search 8 Likelihood: -6914.764209 Slow ML Search 9 Likelihood: -6914.764242 Slow ML optimization finished Slow ML search Time: 69.954710 seconds Thorough ML search Time: 10.154393 seconds Final ML Optimization Likelihood: -6914.764219 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.765089 Tree-Length: 22.506883 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 257.126456 secs or 0.071424 hours Combined Bootstrap and ML search took 482.983845 secs or 0.134162 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.Gymnodinium-catenatum-GC744.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Gymnodinium-catenatum-GC744.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Gymnodinium-catenatum-GC744.MUSCLE All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.Gymnodinium-catenatum-GC744.MUSCLE Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Gymnodinium-catenatum-GC744.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.Gymnodinium-catenatum-GC744.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.Gymnodinium-catenatum-GC744.MUSCLE Overall execution time for full ML analysis: 482.997243 secs or 0.134166 hours or 0.005590 days