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 306 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 72.34% 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: 306 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Chromera-velia-CCMP2878.MUSCLE.fa -n Chromera-velia-CCMP2878.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.170225 Bootstrap[0]: Time 2.701468 seconds, bootstrap likelihood -7314.496147, best rearrangement setting 13 Bootstrap[1]: Time 2.191317 seconds, bootstrap likelihood -7490.716883, best rearrangement setting 13 Bootstrap[2]: Time 2.511048 seconds, bootstrap likelihood -7634.232333, best rearrangement setting 12 Bootstrap[3]: Time 2.527406 seconds, bootstrap likelihood -6428.153751, best rearrangement setting 15 Bootstrap[4]: Time 1.930849 seconds, bootstrap likelihood -6594.902631, best rearrangement setting 10 Bootstrap[5]: Time 2.402099 seconds, bootstrap likelihood -7772.223800, best rearrangement setting 10 Bootstrap[6]: Time 2.359127 seconds, bootstrap likelihood -7169.945206, best rearrangement setting 6 Bootstrap[7]: Time 2.690648 seconds, bootstrap likelihood -7530.234020, best rearrangement setting 14 Bootstrap[8]: Time 2.376602 seconds, bootstrap likelihood -6610.846915, best rearrangement setting 5 Bootstrap[9]: Time 2.314218 seconds, bootstrap likelihood -7392.732538, best rearrangement setting 7 Bootstrap[10]: Time 2.456415 seconds, bootstrap likelihood -7302.751349, best rearrangement setting 7 Bootstrap[11]: Time 2.333399 seconds, bootstrap likelihood -6753.319907, best rearrangement setting 5 Bootstrap[12]: Time 2.127925 seconds, bootstrap likelihood -6938.150056, best rearrangement setting 8 Bootstrap[13]: Time 2.544440 seconds, bootstrap likelihood -6981.442053, best rearrangement setting 7 Bootstrap[14]: Time 2.064996 seconds, bootstrap likelihood -6835.769181, best rearrangement setting 12 Bootstrap[15]: Time 2.091104 seconds, bootstrap likelihood -7068.492564, best rearrangement setting 15 Bootstrap[16]: Time 2.211653 seconds, bootstrap likelihood -6965.531698, best rearrangement setting 12 Bootstrap[17]: Time 2.243614 seconds, bootstrap likelihood -7154.781504, best rearrangement setting 12 Bootstrap[18]: Time 2.103862 seconds, bootstrap likelihood -7127.611923, best rearrangement setting 5 Bootstrap[19]: Time 2.325521 seconds, bootstrap likelihood -6897.176276, best rearrangement setting 8 Bootstrap[20]: Time 2.137153 seconds, bootstrap likelihood -6835.473120, best rearrangement setting 10 Bootstrap[21]: Time 1.956033 seconds, bootstrap likelihood -6405.865055, best rearrangement setting 6 Bootstrap[22]: Time 2.028875 seconds, bootstrap likelihood -7113.764682, best rearrangement setting 5 Bootstrap[23]: Time 2.115617 seconds, bootstrap likelihood -7219.826935, best rearrangement setting 7 Bootstrap[24]: Time 2.591722 seconds, bootstrap likelihood -6944.477452, best rearrangement setting 8 Bootstrap[25]: Time 2.629802 seconds, bootstrap likelihood -7430.367293, best rearrangement setting 6 Bootstrap[26]: Time 2.125149 seconds, bootstrap likelihood -6714.483461, best rearrangement setting 12 Bootstrap[27]: Time 2.324466 seconds, bootstrap likelihood -6571.796835, best rearrangement setting 10 Bootstrap[28]: Time 2.171120 seconds, bootstrap likelihood -7418.789412, best rearrangement setting 11 Bootstrap[29]: Time 2.603126 seconds, bootstrap likelihood -7587.886677, best rearrangement setting 12 Bootstrap[30]: Time 2.553324 seconds, bootstrap likelihood -7267.260937, best rearrangement setting 15 Bootstrap[31]: Time 2.351648 seconds, bootstrap likelihood -6533.111648, best rearrangement setting 15 Bootstrap[32]: Time 1.872257 seconds, bootstrap likelihood -6824.497995, best rearrangement setting 6 Bootstrap[33]: Time 2.433388 seconds, bootstrap likelihood -7212.599148, best rearrangement setting 15 Bootstrap[34]: Time 2.086259 seconds, bootstrap likelihood -6825.808018, best rearrangement setting 11 Bootstrap[35]: Time 2.120308 seconds, bootstrap likelihood -7264.094247, best rearrangement setting 8 Bootstrap[36]: Time 1.869915 seconds, bootstrap likelihood -7059.005137, best rearrangement setting 9 Bootstrap[37]: Time 2.390690 seconds, bootstrap likelihood -7204.231160, best rearrangement setting 11 Bootstrap[38]: Time 2.246873 seconds, bootstrap likelihood -7457.005480, best rearrangement setting 8 Bootstrap[39]: Time 2.232308 seconds, bootstrap likelihood -7094.904672, best rearrangement setting 13 Bootstrap[40]: Time 2.114073 seconds, bootstrap likelihood -6910.430716, best rearrangement setting 13 Bootstrap[41]: Time 2.246717 seconds, bootstrap likelihood -6942.034227, best rearrangement setting 10 Bootstrap[42]: Time 2.272522 seconds, bootstrap likelihood -6638.795277, best rearrangement setting 5 Bootstrap[43]: Time 2.351804 seconds, bootstrap likelihood -7416.843274, best rearrangement setting 14 Bootstrap[44]: Time 2.850077 seconds, bootstrap likelihood -7541.869595, best rearrangement setting 10 Bootstrap[45]: Time 2.643264 seconds, bootstrap likelihood -7478.197870, best rearrangement setting 15 Bootstrap[46]: Time 2.465890 seconds, bootstrap likelihood -7063.222194, best rearrangement setting 14 Bootstrap[47]: Time 2.040988 seconds, bootstrap likelihood -7464.077418, best rearrangement setting 8 Bootstrap[48]: Time 2.258357 seconds, bootstrap likelihood -7530.973445, best rearrangement setting 6 Bootstrap[49]: Time 2.283914 seconds, bootstrap likelihood -7458.304766, best rearrangement setting 7 Bootstrap[50]: Time 2.253759 seconds, bootstrap likelihood -6895.714432, best rearrangement setting 7 Bootstrap[51]: Time 2.397375 seconds, bootstrap likelihood -7160.614149, best rearrangement setting 11 Bootstrap[52]: Time 2.354755 seconds, bootstrap likelihood -7471.552413, best rearrangement setting 12 Bootstrap[53]: Time 2.560546 seconds, bootstrap likelihood -6660.809940, best rearrangement setting 8 Bootstrap[54]: Time 2.261074 seconds, bootstrap likelihood -7356.453657, best rearrangement setting 9 Bootstrap[55]: Time 2.522977 seconds, bootstrap likelihood -7299.101028, best rearrangement setting 11 Bootstrap[56]: Time 2.789520 seconds, bootstrap likelihood -7081.088318, best rearrangement setting 5 Bootstrap[57]: Time 2.256469 seconds, bootstrap likelihood -7323.058763, best rearrangement setting 7 Bootstrap[58]: Time 2.257073 seconds, bootstrap likelihood -6282.595119, best rearrangement setting 10 Bootstrap[59]: Time 2.216455 seconds, bootstrap likelihood -7728.190452, best rearrangement setting 9 Bootstrap[60]: Time 2.450337 seconds, bootstrap likelihood -6637.263392, best rearrangement setting 7 Bootstrap[61]: Time 2.271571 seconds, bootstrap likelihood -7680.345603, best rearrangement setting 5 Bootstrap[62]: Time 2.617057 seconds, bootstrap likelihood -7466.744210, best rearrangement setting 11 Bootstrap[63]: Time 1.959119 seconds, bootstrap likelihood -6872.593157, best rearrangement setting 12 Bootstrap[64]: Time 2.607886 seconds, bootstrap likelihood -7645.508481, best rearrangement setting 7 Bootstrap[65]: Time 2.260346 seconds, bootstrap likelihood -6971.295735, best rearrangement setting 5 Bootstrap[66]: Time 2.004181 seconds, bootstrap likelihood -7110.796338, best rearrangement setting 5 Bootstrap[67]: Time 2.163931 seconds, bootstrap likelihood -7516.082412, best rearrangement setting 15 Bootstrap[68]: Time 2.045033 seconds, bootstrap likelihood -6775.229827, best rearrangement setting 11 Bootstrap[69]: Time 2.291494 seconds, bootstrap likelihood -7336.340950, best rearrangement setting 5 Bootstrap[70]: Time 2.180048 seconds, bootstrap likelihood -6538.663322, best rearrangement setting 8 Bootstrap[71]: Time 2.166701 seconds, bootstrap likelihood -6554.593383, best rearrangement setting 10 Bootstrap[72]: Time 2.287033 seconds, bootstrap likelihood -6592.086845, best rearrangement setting 11 Bootstrap[73]: Time 2.308770 seconds, bootstrap likelihood -7674.287668, best rearrangement setting 9 Bootstrap[74]: Time 1.963362 seconds, bootstrap likelihood -7541.982049, best rearrangement setting 5 Bootstrap[75]: Time 2.255194 seconds, bootstrap likelihood -7913.690958, best rearrangement setting 8 Bootstrap[76]: Time 2.152748 seconds, bootstrap likelihood -7027.074589, best rearrangement setting 9 Bootstrap[77]: Time 2.499680 seconds, bootstrap likelihood -7382.263996, best rearrangement setting 11 Bootstrap[78]: Time 2.098498 seconds, bootstrap likelihood -7470.257979, best rearrangement setting 15 Bootstrap[79]: Time 2.604309 seconds, bootstrap likelihood -7827.298642, best rearrangement setting 9 Bootstrap[80]: Time 2.688571 seconds, bootstrap likelihood -7567.880116, best rearrangement setting 15 Bootstrap[81]: Time 2.179283 seconds, bootstrap likelihood -6742.618940, best rearrangement setting 7 Bootstrap[82]: Time 2.515057 seconds, bootstrap likelihood -6954.861758, best rearrangement setting 6 Bootstrap[83]: Time 2.628665 seconds, bootstrap likelihood -7162.133032, best rearrangement setting 10 Bootstrap[84]: Time 2.435669 seconds, bootstrap likelihood -6661.686527, best rearrangement setting 11 Bootstrap[85]: Time 2.217056 seconds, bootstrap likelihood -7663.899746, best rearrangement setting 8 Bootstrap[86]: Time 2.326287 seconds, bootstrap likelihood -6807.022897, best rearrangement setting 7 Bootstrap[87]: Time 2.363453 seconds, bootstrap likelihood -6630.504146, best rearrangement setting 7 Bootstrap[88]: Time 2.191428 seconds, bootstrap likelihood -7572.798769, best rearrangement setting 12 Bootstrap[89]: Time 2.222592 seconds, bootstrap likelihood -7417.666705, best rearrangement setting 10 Bootstrap[90]: Time 2.123336 seconds, bootstrap likelihood -7381.658920, best rearrangement setting 8 Bootstrap[91]: Time 2.266007 seconds, bootstrap likelihood -6824.765360, best rearrangement setting 12 Bootstrap[92]: Time 2.174397 seconds, bootstrap likelihood -6065.418823, best rearrangement setting 13 Bootstrap[93]: Time 2.341027 seconds, bootstrap likelihood -6594.189582, best rearrangement setting 15 Bootstrap[94]: Time 2.042840 seconds, bootstrap likelihood -6534.341701, best rearrangement setting 5 Bootstrap[95]: Time 2.007594 seconds, bootstrap likelihood -6408.987800, best rearrangement setting 5 Bootstrap[96]: Time 2.303848 seconds, bootstrap likelihood -6734.814303, best rearrangement setting 13 Bootstrap[97]: Time 1.867697 seconds, bootstrap likelihood -5997.821534, best rearrangement setting 11 Bootstrap[98]: Time 2.101054 seconds, bootstrap likelihood -7454.347404, best rearrangement setting 6 Bootstrap[99]: Time 2.291535 seconds, bootstrap likelihood -7022.662217, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 229.289938 seconds Average Time per Rapid Bootstrap 2.292899 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 169.127304 seconds Slow ML Search 0 Likelihood: -7099.066336 Slow ML Search 1 Likelihood: -7099.066336 Slow ML Search 2 Likelihood: -7099.066336 Slow ML Search 3 Likelihood: -7099.066336 Slow ML Search 4 Likelihood: -7099.066336 Slow ML Search 5 Likelihood: -7099.066336 Slow ML Search 6 Likelihood: -7099.066336 Slow ML Search 7 Likelihood: -7099.066336 Slow ML Search 8 Likelihood: -7099.066336 Slow ML Search 9 Likelihood: -7099.066336 Slow ML optimization finished Slow ML search Time: 73.683818 seconds Thorough ML search Time: 11.168818 seconds Final ML Optimization Likelihood: -7099.066757 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.565749 Tree-Length: 25.326682 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 254.066597 secs or 0.070574 hours Combined Bootstrap and ML search took 483.357338 secs or 0.134266 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.Chromera-velia-CCMP2878.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Chromera-velia-CCMP2878.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Chromera-velia-CCMP2878.MUSCLE All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.Chromera-velia-CCMP2878.MUSCLE Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Chromera-velia-CCMP2878.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.Chromera-velia-CCMP2878.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.Chromera-velia-CCMP2878.MUSCLE Overall execution time for full ML analysis: 483.373439 secs or 0.134270 hours or 0.005595 days