IMPORTANT WARNING: Sequences Karenia-brevis-SP3-CAMPEP_0189264108 and Karenia-brevis-Wilson-CAMPEP_0189467908 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-SP3-CAMPEP_0189264108 and Karenia-brevis-SP1-CAMPEP_0189047740 are exactly identical IMPORTANT WARNING: Sequences Bigelowiella-natans-CCMP1258.1_CAMPEP_0172244076 and Bigelowiella-natans-CCMP623_CAMPEP_0169545606 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-SP3-CAMPEP_0189226400 and Karenia-brevis-Wilson-CAMPEP_0189348300 are exactly identical IMPORTANT WARNING Found 4 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. Just in case you might need it, an alignment file with sequence duplicates removed is printed to file H2B-with-other-lineages.muscle.minCov50.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 123 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 3.59% 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: 123 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s H2B-with-other-lineages.muscle.minCov50.fa -n RAxML-H2B-with-other-lineages.muscle.minCov50 -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.151655 Bootstrap[0]: Time 5.684850 seconds, bootstrap likelihood -11104.945961, best rearrangement setting 13 Bootstrap[1]: Time 5.060886 seconds, bootstrap likelihood -10547.312943, best rearrangement setting 13 Bootstrap[2]: Time 4.720380 seconds, bootstrap likelihood -9862.632436, best rearrangement setting 12 Bootstrap[3]: Time 4.603001 seconds, bootstrap likelihood -10107.393232, best rearrangement setting 15 Bootstrap[4]: Time 4.375406 seconds, bootstrap likelihood -10901.739724, best rearrangement setting 10 Bootstrap[5]: Time 5.100691 seconds, bootstrap likelihood -10605.763839, best rearrangement setting 10 Bootstrap[6]: Time 4.121847 seconds, bootstrap likelihood -9534.393238, best rearrangement setting 6 Bootstrap[7]: Time 5.145628 seconds, bootstrap likelihood -10678.509503, best rearrangement setting 14 Bootstrap[8]: Time 4.085228 seconds, bootstrap likelihood -10376.176623, best rearrangement setting 5 Bootstrap[9]: Time 5.146649 seconds, bootstrap likelihood -10804.726863, best rearrangement setting 7 Bootstrap[10]: Time 4.534595 seconds, bootstrap likelihood -10648.221333, best rearrangement setting 7 Bootstrap[11]: Time 4.137845 seconds, bootstrap likelihood -10344.026442, best rearrangement setting 5 Bootstrap[12]: Time 4.626735 seconds, bootstrap likelihood -11287.005392, best rearrangement setting 8 Bootstrap[13]: Time 4.736031 seconds, bootstrap likelihood -10653.563881, best rearrangement setting 7 Bootstrap[14]: Time 4.917150 seconds, bootstrap likelihood -11220.861558, best rearrangement setting 12 Bootstrap[15]: Time 4.943872 seconds, bootstrap likelihood -10515.203399, best rearrangement setting 15 Bootstrap[16]: Time 5.179078 seconds, bootstrap likelihood -10015.232436, best rearrangement setting 12 Bootstrap[17]: Time 5.287470 seconds, bootstrap likelihood -10576.654392, best rearrangement setting 12 Bootstrap[18]: Time 4.907706 seconds, bootstrap likelihood -10330.273404, best rearrangement setting 5 Bootstrap[19]: Time 4.605656 seconds, bootstrap likelihood -10725.456921, best rearrangement setting 8 Bootstrap[20]: Time 4.889810 seconds, bootstrap likelihood -9789.032823, best rearrangement setting 10 Bootstrap[21]: Time 3.785282 seconds, bootstrap likelihood -10598.552057, best rearrangement setting 6 Bootstrap[22]: Time 4.313878 seconds, bootstrap likelihood -11128.205549, best rearrangement setting 5 Bootstrap[23]: Time 4.172745 seconds, bootstrap likelihood -10471.055149, best rearrangement setting 7 Bootstrap[24]: Time 4.523960 seconds, bootstrap likelihood -11505.791827, best rearrangement setting 8 Bootstrap[25]: Time 3.796286 seconds, bootstrap likelihood -11448.594203, best rearrangement setting 6 Bootstrap[26]: Time 5.394946 seconds, bootstrap likelihood -10772.474168, best rearrangement setting 12 Bootstrap[27]: Time 5.257725 seconds, bootstrap likelihood -10790.227979, best rearrangement setting 10 Bootstrap[28]: Time 5.196090 seconds, bootstrap likelihood -10748.194117, best rearrangement setting 11 Bootstrap[29]: Time 4.965675 seconds, bootstrap likelihood -11384.540580, best rearrangement setting 12 Bootstrap[30]: Time 4.258776 seconds, bootstrap likelihood -10624.613726, best rearrangement setting 15 Bootstrap[31]: Time 5.027285 seconds, bootstrap likelihood -10217.374486, best rearrangement setting 15 Bootstrap[32]: Time 5.017414 seconds, bootstrap likelihood -10913.481190, best rearrangement setting 6 Bootstrap[33]: Time 4.712185 seconds, bootstrap likelihood -10096.627122, best rearrangement setting 15 Bootstrap[34]: Time 5.308680 seconds, bootstrap likelihood -11016.839916, best rearrangement setting 11 Bootstrap[35]: Time 5.617201 seconds, bootstrap likelihood -9949.124019, best rearrangement setting 8 Bootstrap[36]: Time 4.731234 seconds, bootstrap likelihood -11307.069135, best rearrangement setting 9 Bootstrap[37]: Time 4.965351 seconds, bootstrap likelihood -9987.398689, best rearrangement setting 11 Bootstrap[38]: Time 5.245683 seconds, bootstrap likelihood -10584.486509, best rearrangement setting 8 Bootstrap[39]: Time 5.298050 seconds, bootstrap likelihood -10687.519539, best rearrangement setting 13 Bootstrap[40]: Time 4.995058 seconds, bootstrap likelihood -10053.983699, best rearrangement setting 13 Bootstrap[41]: Time 4.361336 seconds, bootstrap likelihood -9399.738782, best rearrangement setting 10 Bootstrap[42]: Time 3.976147 seconds, bootstrap likelihood -10881.860400, best rearrangement setting 5 Bootstrap[43]: Time 4.620812 seconds, bootstrap likelihood -11078.836404, best rearrangement setting 14 Bootstrap[44]: Time 4.123894 seconds, bootstrap likelihood -11147.981664, best rearrangement setting 10 Bootstrap[45]: Time 5.173094 seconds, bootstrap likelihood -9972.473736, best rearrangement setting 15 Bootstrap[46]: Time 5.258461 seconds, bootstrap likelihood -10090.374294, best rearrangement setting 14 Bootstrap[47]: Time 4.768896 seconds, bootstrap likelihood -10303.131495, best rearrangement setting 8 Bootstrap[48]: Time 4.298597 seconds, bootstrap likelihood -10226.898934, best rearrangement setting 6 Bootstrap[49]: Time 4.858950 seconds, bootstrap likelihood -10160.790655, best rearrangement setting 7 Bootstrap[50]: Time 4.929124 seconds, bootstrap likelihood -8821.923139, best rearrangement setting 7 Bootstrap[51]: Time 4.937784 seconds, bootstrap likelihood -10850.035759, best rearrangement setting 11 Bootstrap[52]: Time 5.494543 seconds, bootstrap likelihood -11220.218991, best rearrangement setting 12 Bootstrap[53]: Time 4.712628 seconds, bootstrap likelihood -11644.146446, best rearrangement setting 8 Bootstrap[54]: Time 4.894444 seconds, bootstrap likelihood -9968.041193, best rearrangement setting 9 Bootstrap[55]: Time 4.377321 seconds, bootstrap likelihood -10515.301970, best rearrangement setting 11 Bootstrap[56]: Time 4.146802 seconds, bootstrap likelihood -11096.046874, best rearrangement setting 5 Bootstrap[57]: Time 4.470050 seconds, bootstrap likelihood -10380.758993, best rearrangement setting 7 Bootstrap[58]: Time 5.140969 seconds, bootstrap likelihood -11313.306190, best rearrangement setting 10 Bootstrap[59]: Time 4.371441 seconds, bootstrap likelihood -10352.825418, best rearrangement setting 9 Bootstrap[60]: Time 4.444007 seconds, bootstrap likelihood -10957.697158, best rearrangement setting 7 Bootstrap[61]: Time 4.436200 seconds, bootstrap likelihood -10440.756561, best rearrangement setting 5 Bootstrap[62]: Time 4.729630 seconds, bootstrap likelihood -10783.933091, best rearrangement setting 11 Bootstrap[63]: Time 5.368722 seconds, bootstrap likelihood -11212.080183, best rearrangement setting 12 Bootstrap[64]: Time 4.587785 seconds, bootstrap likelihood -10758.134981, best rearrangement setting 7 Bootstrap[65]: Time 3.801246 seconds, bootstrap likelihood -10218.493901, best rearrangement setting 5 Bootstrap[66]: Time 4.649810 seconds, bootstrap likelihood -10328.629950, best rearrangement setting 5 Bootstrap[67]: Time 4.415104 seconds, bootstrap likelihood -10878.440422, best rearrangement setting 15 Bootstrap[68]: Time 5.474991 seconds, bootstrap likelihood -10634.736502, best rearrangement setting 11 Bootstrap[69]: Time 4.367810 seconds, bootstrap likelihood -10333.632797, best rearrangement setting 5 Bootstrap[70]: Time 4.882885 seconds, bootstrap likelihood -10729.080780, best rearrangement setting 8 Bootstrap[71]: Time 4.565857 seconds, bootstrap likelihood -10566.023713, best rearrangement setting 10 Bootstrap[72]: Time 5.382894 seconds, bootstrap likelihood -10536.919238, best rearrangement setting 11 Bootstrap[73]: Time 4.913895 seconds, bootstrap likelihood -10533.560668, best rearrangement setting 9 Bootstrap[74]: Time 4.621621 seconds, bootstrap likelihood -9753.646653, best rearrangement setting 5 Bootstrap[75]: Time 4.815438 seconds, bootstrap likelihood -10102.357414, best rearrangement setting 8 Bootstrap[76]: Time 4.514318 seconds, bootstrap likelihood -10599.824379, best rearrangement setting 9 Bootstrap[77]: Time 4.399318 seconds, bootstrap likelihood -9926.607734, best rearrangement setting 11 Bootstrap[78]: Time 4.650114 seconds, bootstrap likelihood -11518.775724, best rearrangement setting 15 Bootstrap[79]: Time 5.006290 seconds, bootstrap likelihood -10573.214417, best rearrangement setting 9 Bootstrap[80]: Time 3.864041 seconds, bootstrap likelihood -11958.427972, best rearrangement setting 15 Bootstrap[81]: Time 3.991658 seconds, bootstrap likelihood -11016.620085, best rearrangement setting 7 Bootstrap[82]: Time 4.282399 seconds, bootstrap likelihood -9482.152773, best rearrangement setting 6 Bootstrap[83]: Time 5.241196 seconds, bootstrap likelihood -11127.400884, best rearrangement setting 10 Bootstrap[84]: Time 5.009394 seconds, bootstrap likelihood -10319.197802, best rearrangement setting 11 Bootstrap[85]: Time 5.228578 seconds, bootstrap likelihood -10177.518278, best rearrangement setting 8 Bootstrap[86]: Time 4.736400 seconds, bootstrap likelihood -10204.055851, best rearrangement setting 7 Bootstrap[87]: Time 4.578135 seconds, bootstrap likelihood -9653.455886, best rearrangement setting 7 Bootstrap[88]: Time 5.418757 seconds, bootstrap likelihood -10443.761106, best rearrangement setting 12 Bootstrap[89]: Time 5.008362 seconds, bootstrap likelihood -10499.787488, best rearrangement setting 10 Bootstrap[90]: Time 4.299019 seconds, bootstrap likelihood -11693.900444, best rearrangement setting 8 Bootstrap[91]: Time 5.136461 seconds, bootstrap likelihood -10637.423621, best rearrangement setting 12 Bootstrap[92]: Time 5.405523 seconds, bootstrap likelihood -10761.748819, best rearrangement setting 13 Bootstrap[93]: Time 4.919833 seconds, bootstrap likelihood -10609.155796, best rearrangement setting 15 Bootstrap[94]: Time 4.444026 seconds, bootstrap likelihood -10254.168913, best rearrangement setting 5 Bootstrap[95]: Time 4.591791 seconds, bootstrap likelihood -10892.805582, best rearrangement setting 5 Bootstrap[96]: Time 5.190808 seconds, bootstrap likelihood -10826.676566, best rearrangement setting 13 Bootstrap[97]: Time 3.932722 seconds, bootstrap likelihood -11611.257784, best rearrangement setting 11 Bootstrap[98]: Time 5.050086 seconds, bootstrap likelihood -11290.970647, best rearrangement setting 6 Bootstrap[99]: Time 5.305086 seconds, bootstrap likelihood -10425.865411, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 476.086056 seconds Average Time per Rapid Bootstrap 4.760861 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 820.976790 seconds Slow ML Search 0 Likelihood: -10725.186438 Slow ML Search 1 Likelihood: -10726.845848 Slow ML Search 2 Likelihood: -10727.971309 Slow ML Search 3 Likelihood: -10727.951162 Slow ML Search 4 Likelihood: -10727.799527 Slow ML Search 5 Likelihood: -10727.847471 Slow ML Search 6 Likelihood: -10727.965680 Slow ML Search 7 Likelihood: -10728.075301 Slow ML Search 8 Likelihood: -10728.009979 Slow ML Search 9 Likelihood: -10728.689236 Slow ML optimization finished Slow ML search Time: 227.959246 seconds Thorough ML search Time: 17.471709 seconds Final ML Optimization Likelihood: -10725.186665 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.914988 Tree-Length: 52.459216 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 1066.513242 secs or 0.296254 hours Combined Bootstrap and ML search took 1542.600270 secs or 0.428500 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.RAxML-H2B-with-other-lineages.muscle.minCov50 Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.RAxML-H2B-with-other-lineages.muscle.minCov50 Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.RAxML-H2B-with-other-lineages.muscle.minCov50 All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.RAxML-H2B-with-other-lineages.muscle.minCov50 Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.RAxML-H2B-with-other-lineages.muscle.minCov50 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.RAxML-H2B-with-other-lineages.muscle.minCov50 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.RAxML-H2B-with-other-lineages.muscle.minCov50 Overall execution time for full ML analysis: 1542.657766 secs or 0.428516 hours or 0.017855 days