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 308 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 71.12% 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: 308 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Scrippsiella-hangoei-SHTV5.MUSCLE.fa -n Scrippsiella-hangoei-SHTV5.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.151551 Bootstrap[0]: Time 2.414172 seconds, bootstrap likelihood -6840.999317, best rearrangement setting 13 Bootstrap[1]: Time 2.305880 seconds, bootstrap likelihood -6379.712568, best rearrangement setting 13 Bootstrap[2]: Time 2.586954 seconds, bootstrap likelihood -7620.285732, best rearrangement setting 12 Bootstrap[3]: Time 2.424124 seconds, bootstrap likelihood -5835.622280, best rearrangement setting 15 Bootstrap[4]: Time 2.184417 seconds, bootstrap likelihood -6497.349570, best rearrangement setting 10 Bootstrap[5]: Time 2.829912 seconds, bootstrap likelihood -6700.683375, best rearrangement setting 10 Bootstrap[6]: Time 1.990792 seconds, bootstrap likelihood -6494.228247, best rearrangement setting 6 Bootstrap[7]: Time 1.949649 seconds, bootstrap likelihood -6729.359259, best rearrangement setting 14 Bootstrap[8]: Time 2.020320 seconds, bootstrap likelihood -6539.206562, best rearrangement setting 5 Bootstrap[9]: Time 2.640322 seconds, bootstrap likelihood -6406.577949, best rearrangement setting 7 Bootstrap[10]: Time 2.176903 seconds, bootstrap likelihood -6415.523220, best rearrangement setting 7 Bootstrap[11]: Time 2.261110 seconds, bootstrap likelihood -6505.215120, best rearrangement setting 5 Bootstrap[12]: Time 2.245879 seconds, bootstrap likelihood -6380.759728, best rearrangement setting 8 Bootstrap[13]: Time 2.230302 seconds, bootstrap likelihood -6775.099264, best rearrangement setting 7 Bootstrap[14]: Time 2.175247 seconds, bootstrap likelihood -6679.526215, best rearrangement setting 12 Bootstrap[15]: Time 2.433312 seconds, bootstrap likelihood -6510.238251, best rearrangement setting 15 Bootstrap[16]: Time 1.759526 seconds, bootstrap likelihood -6154.554699, best rearrangement setting 12 Bootstrap[17]: Time 2.501328 seconds, bootstrap likelihood -6731.811910, best rearrangement setting 12 Bootstrap[18]: Time 2.292017 seconds, bootstrap likelihood -6766.682904, best rearrangement setting 5 Bootstrap[19]: Time 2.199157 seconds, bootstrap likelihood -6153.602580, best rearrangement setting 8 Bootstrap[20]: Time 2.081258 seconds, bootstrap likelihood -6967.325926, best rearrangement setting 10 Bootstrap[21]: Time 2.218767 seconds, bootstrap likelihood -6178.329789, best rearrangement setting 6 Bootstrap[22]: Time 2.280467 seconds, bootstrap likelihood -6215.822200, best rearrangement setting 5 Bootstrap[23]: Time 2.167561 seconds, bootstrap likelihood -6243.056510, best rearrangement setting 7 Bootstrap[24]: Time 1.811860 seconds, bootstrap likelihood -6618.064986, best rearrangement setting 8 Bootstrap[25]: Time 2.023025 seconds, bootstrap likelihood -6680.044292, best rearrangement setting 6 Bootstrap[26]: Time 2.556606 seconds, bootstrap likelihood -6412.490226, best rearrangement setting 12 Bootstrap[27]: Time 2.248805 seconds, bootstrap likelihood -6536.678675, best rearrangement setting 10 Bootstrap[28]: Time 2.236787 seconds, bootstrap likelihood -5929.116807, best rearrangement setting 11 Bootstrap[29]: Time 2.661783 seconds, bootstrap likelihood -6909.062473, best rearrangement setting 12 Bootstrap[30]: Time 2.378766 seconds, bootstrap likelihood -7041.590026, best rearrangement setting 15 Bootstrap[31]: Time 1.984315 seconds, bootstrap likelihood -6764.215582, best rearrangement setting 15 Bootstrap[32]: Time 2.419254 seconds, bootstrap likelihood -6288.970250, best rearrangement setting 6 Bootstrap[33]: Time 2.272733 seconds, bootstrap likelihood -6275.943308, best rearrangement setting 15 Bootstrap[34]: Time 2.102248 seconds, bootstrap likelihood -6668.841177, best rearrangement setting 11 Bootstrap[35]: Time 2.777651 seconds, bootstrap likelihood -6845.288584, best rearrangement setting 8 Bootstrap[36]: Time 2.768269 seconds, bootstrap likelihood -6041.682298, best rearrangement setting 9 Bootstrap[37]: Time 2.334694 seconds, bootstrap likelihood -6941.609206, best rearrangement setting 11 Bootstrap[38]: Time 2.306948 seconds, bootstrap likelihood -6338.055516, best rearrangement setting 8 Bootstrap[39]: Time 2.630846 seconds, bootstrap likelihood -7281.812386, best rearrangement setting 13 Bootstrap[40]: Time 2.146286 seconds, bootstrap likelihood -6210.125336, best rearrangement setting 13 Bootstrap[41]: Time 2.627804 seconds, bootstrap likelihood -6792.648911, best rearrangement setting 10 Bootstrap[42]: Time 1.992213 seconds, bootstrap likelihood -6498.850323, best rearrangement setting 5 Bootstrap[43]: Time 1.858204 seconds, bootstrap likelihood -6426.477364, best rearrangement setting 14 Bootstrap[44]: Time 2.651458 seconds, bootstrap likelihood -6974.014837, best rearrangement setting 10 Bootstrap[45]: Time 2.415618 seconds, bootstrap likelihood -6996.351137, best rearrangement setting 15 Bootstrap[46]: Time 2.403474 seconds, bootstrap likelihood -6195.498857, best rearrangement setting 14 Bootstrap[47]: Time 2.614396 seconds, bootstrap likelihood -6530.886947, best rearrangement setting 8 Bootstrap[48]: Time 2.053506 seconds, bootstrap likelihood -6601.969043, best rearrangement setting 6 Bootstrap[49]: Time 2.293656 seconds, bootstrap likelihood -7427.593302, best rearrangement setting 7 Bootstrap[50]: Time 2.481643 seconds, bootstrap likelihood -7149.508904, best rearrangement setting 7 Bootstrap[51]: Time 2.527597 seconds, bootstrap likelihood -6093.406882, best rearrangement setting 11 Bootstrap[52]: Time 2.507696 seconds, bootstrap likelihood -6326.249676, best rearrangement setting 12 Bootstrap[53]: Time 2.403677 seconds, bootstrap likelihood -6996.770301, best rearrangement setting 8 Bootstrap[54]: Time 2.635221 seconds, bootstrap likelihood -6587.635633, best rearrangement setting 9 Bootstrap[55]: Time 2.407341 seconds, bootstrap likelihood -6153.202056, best rearrangement setting 11 Bootstrap[56]: Time 2.127151 seconds, bootstrap likelihood -7054.100611, best rearrangement setting 5 Bootstrap[57]: Time 2.280267 seconds, bootstrap likelihood -6434.911728, best rearrangement setting 7 Bootstrap[58]: Time 2.612790 seconds, bootstrap likelihood -6426.356587, best rearrangement setting 10 Bootstrap[59]: Time 2.831751 seconds, bootstrap likelihood -6523.880213, best rearrangement setting 9 Bootstrap[60]: Time 2.311281 seconds, bootstrap likelihood -6419.619084, best rearrangement setting 7 Bootstrap[61]: Time 1.976047 seconds, bootstrap likelihood -6141.234300, best rearrangement setting 5 Bootstrap[62]: Time 1.980075 seconds, bootstrap likelihood -6375.287511, best rearrangement setting 11 Bootstrap[63]: Time 2.625447 seconds, bootstrap likelihood -6848.301007, best rearrangement setting 12 Bootstrap[64]: Time 2.200614 seconds, bootstrap likelihood -6556.548613, best rearrangement setting 7 Bootstrap[65]: Time 2.253392 seconds, bootstrap likelihood -6133.192901, best rearrangement setting 5 Bootstrap[66]: Time 2.265456 seconds, bootstrap likelihood -6678.742401, best rearrangement setting 5 Bootstrap[67]: Time 1.842155 seconds, bootstrap likelihood -6759.173617, best rearrangement setting 15 Bootstrap[68]: Time 2.036682 seconds, bootstrap likelihood -6338.799839, best rearrangement setting 11 Bootstrap[69]: Time 2.321774 seconds, bootstrap likelihood -6670.363251, best rearrangement setting 5 Bootstrap[70]: Time 2.341870 seconds, bootstrap likelihood -6799.836744, best rearrangement setting 8 Bootstrap[71]: Time 2.328217 seconds, bootstrap likelihood -6617.113064, best rearrangement setting 10 Bootstrap[72]: Time 2.434813 seconds, bootstrap likelihood -6062.189281, best rearrangement setting 11 Bootstrap[73]: Time 2.253852 seconds, bootstrap likelihood -6280.634616, best rearrangement setting 9 Bootstrap[74]: Time 2.076219 seconds, bootstrap likelihood -6255.873534, best rearrangement setting 5 Bootstrap[75]: Time 2.324996 seconds, bootstrap likelihood -6875.737068, best rearrangement setting 8 Bootstrap[76]: Time 2.328806 seconds, bootstrap likelihood -6983.282069, best rearrangement setting 9 Bootstrap[77]: Time 1.992541 seconds, bootstrap likelihood -7061.871100, best rearrangement setting 11 Bootstrap[78]: Time 2.287801 seconds, bootstrap likelihood -6568.213844, best rearrangement setting 15 Bootstrap[79]: Time 2.330040 seconds, bootstrap likelihood -6803.655855, best rearrangement setting 9 Bootstrap[80]: Time 1.764840 seconds, bootstrap likelihood -6896.047120, best rearrangement setting 15 Bootstrap[81]: Time 2.241019 seconds, bootstrap likelihood -6727.594100, best rearrangement setting 7 Bootstrap[82]: Time 2.525016 seconds, bootstrap likelihood -7098.614090, best rearrangement setting 6 Bootstrap[83]: Time 2.161694 seconds, bootstrap likelihood -6415.360340, best rearrangement setting 10 Bootstrap[84]: Time 2.095001 seconds, bootstrap likelihood -6028.948423, best rearrangement setting 11 Bootstrap[85]: Time 2.973800 seconds, bootstrap likelihood -6485.263192, best rearrangement setting 8 Bootstrap[86]: Time 2.297312 seconds, bootstrap likelihood -6584.702173, best rearrangement setting 7 Bootstrap[87]: Time 2.121981 seconds, bootstrap likelihood -6680.695842, best rearrangement setting 7 Bootstrap[88]: Time 2.227757 seconds, bootstrap likelihood -6639.962663, best rearrangement setting 12 Bootstrap[89]: Time 2.291362 seconds, bootstrap likelihood -5852.138227, best rearrangement setting 10 Bootstrap[90]: Time 2.238779 seconds, bootstrap likelihood -7013.679955, best rearrangement setting 8 Bootstrap[91]: Time 2.508290 seconds, bootstrap likelihood -6835.389265, best rearrangement setting 12 Bootstrap[92]: Time 2.323462 seconds, bootstrap likelihood -6282.979380, best rearrangement setting 13 Bootstrap[93]: Time 2.294900 seconds, bootstrap likelihood -6750.020649, best rearrangement setting 15 Bootstrap[94]: Time 1.872664 seconds, bootstrap likelihood -5743.843398, best rearrangement setting 5 Bootstrap[95]: Time 2.530409 seconds, bootstrap likelihood -6762.110754, best rearrangement setting 5 Bootstrap[96]: Time 2.258685 seconds, bootstrap likelihood -6310.727553, best rearrangement setting 13 Bootstrap[97]: Time 2.307963 seconds, bootstrap likelihood -6547.613077, best rearrangement setting 11 Bootstrap[98]: Time 2.521710 seconds, bootstrap likelihood -5834.670354, best rearrangement setting 6 Bootstrap[99]: Time 2.320526 seconds, bootstrap likelihood -5973.534297, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 230.223966 seconds Average Time per Rapid Bootstrap 2.302240 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 176.982735 seconds Slow ML Search 0 Likelihood: -6555.443630 Slow ML Search 1 Likelihood: -6555.443630 Slow ML Search 2 Likelihood: -6555.443630 Slow ML Search 3 Likelihood: -6555.443630 Slow ML Search 4 Likelihood: -6555.443630 Slow ML Search 5 Likelihood: -6555.443630 Slow ML Search 6 Likelihood: -6555.443630 Slow ML Search 7 Likelihood: -6555.443630 Slow ML Search 8 Likelihood: -6555.443630 Slow ML Search 9 Likelihood: -6555.443630 Slow ML optimization finished Slow ML search Time: 65.835418 seconds Thorough ML search Time: 8.982406 seconds Final ML Optimization Likelihood: -6555.445742 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.492280 Tree-Length: 25.676267 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 251.890921 secs or 0.069970 hours Combined Bootstrap and ML search took 482.115731 secs or 0.133921 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.Scrippsiella-hangoei-SHTV5.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Scrippsiella-hangoei-SHTV5.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Scrippsiella-hangoei-SHTV5.MUSCLE All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.Scrippsiella-hangoei-SHTV5.MUSCLE Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Scrippsiella-hangoei-SHTV5.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.Scrippsiella-hangoei-SHTV5.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.Scrippsiella-hangoei-SHTV5.MUSCLE Overall execution time for full ML analysis: 482.129782 secs or 0.133925 hours or 0.005580 days