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 268 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 72.10% 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: 268 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Glenodinium-foliaceum-CCAP1116_3.MUSCLE.fa -n Glenodinium-foliaceum-CCAP1116_3.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.074048 Bootstrap[0]: Time 2.798971 seconds, bootstrap likelihood -6359.734365, best rearrangement setting 13 Bootstrap[1]: Time 2.607237 seconds, bootstrap likelihood -6479.549631, best rearrangement setting 13 Bootstrap[2]: Time 2.565121 seconds, bootstrap likelihood -7262.043063, best rearrangement setting 12 Bootstrap[3]: Time 2.436339 seconds, bootstrap likelihood -5859.814561, best rearrangement setting 15 Bootstrap[4]: Time 2.549296 seconds, bootstrap likelihood -6389.641836, best rearrangement setting 10 Bootstrap[5]: Time 2.469806 seconds, bootstrap likelihood -6814.173616, best rearrangement setting 10 Bootstrap[6]: Time 2.209474 seconds, bootstrap likelihood -6228.393771, best rearrangement setting 6 Bootstrap[7]: Time 2.513891 seconds, bootstrap likelihood -6372.620130, best rearrangement setting 14 Bootstrap[8]: Time 2.652178 seconds, bootstrap likelihood -6140.568877, best rearrangement setting 5 Bootstrap[9]: Time 2.226038 seconds, bootstrap likelihood -5988.650059, best rearrangement setting 7 Bootstrap[10]: Time 2.159647 seconds, bootstrap likelihood -6360.564861, best rearrangement setting 7 Bootstrap[11]: Time 1.893091 seconds, bootstrap likelihood -6501.403498, best rearrangement setting 5 Bootstrap[12]: Time 2.345548 seconds, bootstrap likelihood -6090.841342, best rearrangement setting 8 Bootstrap[13]: Time 2.469015 seconds, bootstrap likelihood -6342.374405, best rearrangement setting 7 Bootstrap[14]: Time 2.535197 seconds, bootstrap likelihood -6344.539078, best rearrangement setting 12 Bootstrap[15]: Time 2.186426 seconds, bootstrap likelihood -6481.112315, best rearrangement setting 15 Bootstrap[16]: Time 2.464506 seconds, bootstrap likelihood -6051.755385, best rearrangement setting 12 Bootstrap[17]: Time 2.376698 seconds, bootstrap likelihood -6491.492650, best rearrangement setting 12 Bootstrap[18]: Time 2.112376 seconds, bootstrap likelihood -6453.996836, best rearrangement setting 5 Bootstrap[19]: Time 2.534167 seconds, bootstrap likelihood -6073.901215, best rearrangement setting 8 Bootstrap[20]: Time 1.995007 seconds, bootstrap likelihood -6502.153260, best rearrangement setting 10 Bootstrap[21]: Time 2.526436 seconds, bootstrap likelihood -6187.104163, best rearrangement setting 6 Bootstrap[22]: Time 2.962424 seconds, bootstrap likelihood -6366.344295, best rearrangement setting 5 Bootstrap[23]: Time 2.535317 seconds, bootstrap likelihood -6195.654640, best rearrangement setting 7 Bootstrap[24]: Time 2.323690 seconds, bootstrap likelihood -6587.917431, best rearrangement setting 8 Bootstrap[25]: Time 2.083523 seconds, bootstrap likelihood -6347.988647, best rearrangement setting 6 Bootstrap[26]: Time 2.389873 seconds, bootstrap likelihood -6142.624919, best rearrangement setting 12 Bootstrap[27]: Time 2.354095 seconds, bootstrap likelihood -5824.825931, best rearrangement setting 10 Bootstrap[28]: Time 2.453831 seconds, bootstrap likelihood -5708.776975, best rearrangement setting 11 Bootstrap[29]: Time 2.742655 seconds, bootstrap likelihood -6668.865772, best rearrangement setting 12 Bootstrap[30]: Time 2.359129 seconds, bootstrap likelihood -6696.992056, best rearrangement setting 15 Bootstrap[31]: Time 2.847488 seconds, bootstrap likelihood -6533.000645, best rearrangement setting 15 Bootstrap[32]: Time 2.609230 seconds, bootstrap likelihood -5893.692693, best rearrangement setting 6 Bootstrap[33]: Time 2.270507 seconds, bootstrap likelihood -6337.334635, best rearrangement setting 15 Bootstrap[34]: Time 2.591127 seconds, bootstrap likelihood -6745.942272, best rearrangement setting 11 Bootstrap[35]: Time 2.604736 seconds, bootstrap likelihood -6248.810232, best rearrangement setting 8 Bootstrap[36]: Time 2.383953 seconds, bootstrap likelihood -5996.703393, best rearrangement setting 9 Bootstrap[37]: Time 2.486340 seconds, bootstrap likelihood -6787.500503, best rearrangement setting 11 Bootstrap[38]: Time 2.420129 seconds, bootstrap likelihood -6199.524307, best rearrangement setting 8 Bootstrap[39]: Time 2.824925 seconds, bootstrap likelihood -6844.797914, best rearrangement setting 13 Bootstrap[40]: Time 2.682316 seconds, bootstrap likelihood -6033.486455, best rearrangement setting 13 Bootstrap[41]: Time 2.749091 seconds, bootstrap likelihood -6881.801425, best rearrangement setting 10 Bootstrap[42]: Time 2.241406 seconds, bootstrap likelihood -6344.008079, best rearrangement setting 5 Bootstrap[43]: Time 2.533249 seconds, bootstrap likelihood -6278.322033, best rearrangement setting 14 Bootstrap[44]: Time 2.652446 seconds, bootstrap likelihood -6520.326224, best rearrangement setting 10 Bootstrap[45]: Time 3.010360 seconds, bootstrap likelihood -7058.032423, best rearrangement setting 15 Bootstrap[46]: Time 3.080351 seconds, bootstrap likelihood -7146.952469, best rearrangement setting 14 Bootstrap[47]: Time 2.799961 seconds, bootstrap likelihood -6196.200034, best rearrangement setting 8 Bootstrap[48]: Time 2.716357 seconds, bootstrap likelihood -6449.396846, best rearrangement setting 6 Bootstrap[49]: Time 3.091404 seconds, bootstrap likelihood -7369.562366, best rearrangement setting 7 Bootstrap[50]: Time 2.466434 seconds, bootstrap likelihood -7150.676202, best rearrangement setting 7 Bootstrap[51]: Time 2.275892 seconds, bootstrap likelihood -6045.965470, best rearrangement setting 11 Bootstrap[52]: Time 2.095405 seconds, bootstrap likelihood -6193.048463, best rearrangement setting 12 Bootstrap[53]: Time 1.951849 seconds, bootstrap likelihood -6901.888170, best rearrangement setting 8 Bootstrap[54]: Time 2.015949 seconds, bootstrap likelihood -6624.998137, best rearrangement setting 9 Bootstrap[55]: Time 2.144600 seconds, bootstrap likelihood -6156.149193, best rearrangement setting 11 Bootstrap[56]: Time 2.183636 seconds, bootstrap likelihood -6431.661687, best rearrangement setting 5 Bootstrap[57]: Time 2.371228 seconds, bootstrap likelihood -6605.440830, best rearrangement setting 7 Bootstrap[58]: Time 2.381325 seconds, bootstrap likelihood -5860.603797, best rearrangement setting 10 Bootstrap[59]: Time 2.974092 seconds, bootstrap likelihood -6641.615057, best rearrangement setting 9 Bootstrap[60]: Time 2.907949 seconds, bootstrap likelihood -6388.223559, best rearrangement setting 7 Bootstrap[61]: Time 2.212073 seconds, bootstrap likelihood -6482.068369, best rearrangement setting 5 Bootstrap[62]: Time 2.585622 seconds, bootstrap likelihood -6069.154128, best rearrangement setting 11 Bootstrap[63]: Time 2.038456 seconds, bootstrap likelihood -6669.380436, best rearrangement setting 12 Bootstrap[64]: Time 2.697959 seconds, bootstrap likelihood -6426.033695, best rearrangement setting 7 Bootstrap[65]: Time 2.127689 seconds, bootstrap likelihood -6413.181253, best rearrangement setting 5 Bootstrap[66]: Time 2.418915 seconds, bootstrap likelihood -6792.437007, best rearrangement setting 5 Bootstrap[67]: Time 2.750701 seconds, bootstrap likelihood -6666.250001, best rearrangement setting 15 Bootstrap[68]: Time 1.984958 seconds, bootstrap likelihood -5790.016649, best rearrangement setting 11 Bootstrap[69]: Time 2.523686 seconds, bootstrap likelihood -6717.180709, best rearrangement setting 5 Bootstrap[70]: Time 2.261191 seconds, bootstrap likelihood -5730.695304, best rearrangement setting 8 Bootstrap[71]: Time 2.216676 seconds, bootstrap likelihood -6304.461562, best rearrangement setting 10 Bootstrap[72]: Time 2.241865 seconds, bootstrap likelihood -6440.354214, best rearrangement setting 11 Bootstrap[73]: Time 2.033864 seconds, bootstrap likelihood -6273.792871, best rearrangement setting 9 Bootstrap[74]: Time 2.481219 seconds, bootstrap likelihood -6419.575778, best rearrangement setting 5 Bootstrap[75]: Time 2.116348 seconds, bootstrap likelihood -6434.038967, best rearrangement setting 8 Bootstrap[76]: Time 2.600346 seconds, bootstrap likelihood -6878.978742, best rearrangement setting 9 Bootstrap[77]: Time 2.848031 seconds, bootstrap likelihood -6811.373158, best rearrangement setting 11 Bootstrap[78]: Time 2.475560 seconds, bootstrap likelihood -6345.757071, best rearrangement setting 15 Bootstrap[79]: Time 2.534902 seconds, bootstrap likelihood -6850.107321, best rearrangement setting 9 Bootstrap[80]: Time 2.464502 seconds, bootstrap likelihood -7040.543042, best rearrangement setting 15 Bootstrap[81]: Time 2.156014 seconds, bootstrap likelihood -6542.148183, best rearrangement setting 7 Bootstrap[82]: Time 2.265953 seconds, bootstrap likelihood -6685.811876, best rearrangement setting 6 Bootstrap[83]: Time 2.131104 seconds, bootstrap likelihood -6071.898941, best rearrangement setting 10 Bootstrap[84]: Time 2.593511 seconds, bootstrap likelihood -6110.066269, best rearrangement setting 11 Bootstrap[85]: Time 2.104044 seconds, bootstrap likelihood -5790.047669, best rearrangement setting 8 Bootstrap[86]: Time 2.658945 seconds, bootstrap likelihood -7162.668349, best rearrangement setting 7 Bootstrap[87]: Time 1.968602 seconds, bootstrap likelihood -6420.486983, best rearrangement setting 7 Bootstrap[88]: Time 2.794537 seconds, bootstrap likelihood -6630.618537, best rearrangement setting 12 Bootstrap[89]: Time 2.239937 seconds, bootstrap likelihood -5873.084312, best rearrangement setting 10 Bootstrap[90]: Time 2.559931 seconds, bootstrap likelihood -6863.386744, best rearrangement setting 8 Bootstrap[91]: Time 2.315631 seconds, bootstrap likelihood -7280.365567, best rearrangement setting 12 Bootstrap[92]: Time 2.765746 seconds, bootstrap likelihood -6555.938805, best rearrangement setting 13 Bootstrap[93]: Time 2.139724 seconds, bootstrap likelihood -6854.396110, best rearrangement setting 15 Bootstrap[94]: Time 2.328060 seconds, bootstrap likelihood -6127.873304, best rearrangement setting 5 Bootstrap[95]: Time 2.051877 seconds, bootstrap likelihood -6183.288656, best rearrangement setting 5 Bootstrap[96]: Time 2.603771 seconds, bootstrap likelihood -6391.189801, best rearrangement setting 13 Bootstrap[97]: Time 2.663390 seconds, bootstrap likelihood -6538.798330, best rearrangement setting 11 Bootstrap[98]: Time 2.389118 seconds, bootstrap likelihood -5849.789724, best rearrangement setting 6 Bootstrap[99]: Time 2.218430 seconds, bootstrap likelihood -6180.585760, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 243.835760 seconds Average Time per Rapid Bootstrap 2.438358 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 240.678258 seconds Slow ML Search 0 Likelihood: -6472.546118 Slow ML Search 1 Likelihood: -6472.546118 Slow ML Search 2 Likelihood: -6472.546140 Slow ML Search 3 Likelihood: -6472.546134 Slow ML Search 4 Likelihood: -6472.546113 Slow ML Search 5 Likelihood: -6472.546113 Slow ML Search 6 Likelihood: -6472.546119 Slow ML Search 7 Likelihood: -6472.546136 Slow ML Search 8 Likelihood: -6472.546215 Slow ML Search 9 Likelihood: -6472.546216 Slow ML optimization finished Slow ML search Time: 93.337688 seconds Thorough ML search Time: 9.439754 seconds Final ML Optimization Likelihood: -6472.547753 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.434812 Tree-Length: 25.866440 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 343.544658 secs or 0.095429 hours Combined Bootstrap and ML search took 587.381203 secs or 0.163161 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.Glenodinium-foliaceum-CCAP1116_3.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Glenodinium-foliaceum-CCAP1116_3.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Glenodinium-foliaceum-CCAP1116_3.MUSCLE All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.Glenodinium-foliaceum-CCAP1116_3.MUSCLE Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Glenodinium-foliaceum-CCAP1116_3.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.Glenodinium-foliaceum-CCAP1116_3.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.Glenodinium-foliaceum-CCAP1116_3.MUSCLE Overall execution time for full ML analysis: 587.395010 secs or 0.163165 hours or 0.006799 days