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 399 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 75.48% 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: 399 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s Symbiodinium-sp-Mp.MUSCLE.fa -n Symbiodinium-sp-Mp.MUSCLE -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.197304 Bootstrap[0]: Time 3.227328 seconds, bootstrap likelihood -8467.182201, best rearrangement setting 13 Bootstrap[1]: Time 2.850692 seconds, bootstrap likelihood -9134.567033, best rearrangement setting 13 Bootstrap[2]: Time 2.442886 seconds, bootstrap likelihood -8441.634529, best rearrangement setting 12 Bootstrap[3]: Time 2.909502 seconds, bootstrap likelihood -8492.376760, best rearrangement setting 15 Bootstrap[4]: Time 2.313234 seconds, bootstrap likelihood -9237.484707, best rearrangement setting 10 Bootstrap[5]: Time 3.066620 seconds, bootstrap likelihood -8400.517112, best rearrangement setting 10 Bootstrap[6]: Time 2.637096 seconds, bootstrap likelihood -8650.365155, best rearrangement setting 6 Bootstrap[7]: Time 2.609374 seconds, bootstrap likelihood -8000.751132, best rearrangement setting 14 Bootstrap[8]: Time 2.818823 seconds, bootstrap likelihood -8391.297065, best rearrangement setting 5 Bootstrap[9]: Time 2.743284 seconds, bootstrap likelihood -8587.270902, best rearrangement setting 7 Bootstrap[10]: Time 2.622215 seconds, bootstrap likelihood -8064.268459, best rearrangement setting 7 Bootstrap[11]: Time 2.391615 seconds, bootstrap likelihood -8607.184685, best rearrangement setting 5 Bootstrap[12]: Time 2.740930 seconds, bootstrap likelihood -8918.213651, best rearrangement setting 8 Bootstrap[13]: Time 2.196766 seconds, bootstrap likelihood -7691.236470, best rearrangement setting 7 Bootstrap[14]: Time 2.874021 seconds, bootstrap likelihood -8648.356162, best rearrangement setting 12 Bootstrap[15]: Time 2.839742 seconds, bootstrap likelihood -7910.947593, best rearrangement setting 15 Bootstrap[16]: Time 2.882459 seconds, bootstrap likelihood -8843.226099, best rearrangement setting 12 Bootstrap[17]: Time 3.072153 seconds, bootstrap likelihood -8208.176714, best rearrangement setting 12 Bootstrap[18]: Time 3.013794 seconds, bootstrap likelihood -8495.703721, best rearrangement setting 5 Bootstrap[19]: Time 2.931723 seconds, bootstrap likelihood -8728.959970, best rearrangement setting 8 Bootstrap[20]: Time 2.761060 seconds, bootstrap likelihood -8229.957254, best rearrangement setting 10 Bootstrap[21]: Time 3.310496 seconds, bootstrap likelihood -8380.011878, best rearrangement setting 6 Bootstrap[22]: Time 2.981077 seconds, bootstrap likelihood -8027.360300, best rearrangement setting 5 Bootstrap[23]: Time 2.622301 seconds, bootstrap likelihood -8374.146778, best rearrangement setting 7 Bootstrap[24]: Time 2.482079 seconds, bootstrap likelihood -9023.664787, best rearrangement setting 8 Bootstrap[25]: Time 2.868794 seconds, bootstrap likelihood -8501.598336, best rearrangement setting 6 Bootstrap[26]: Time 3.034539 seconds, bootstrap likelihood -8475.542198, best rearrangement setting 12 Bootstrap[27]: Time 2.758541 seconds, bootstrap likelihood -8550.568398, best rearrangement setting 10 Bootstrap[28]: Time 2.809514 seconds, bootstrap likelihood -8471.427640, best rearrangement setting 11 Bootstrap[29]: Time 3.122917 seconds, bootstrap likelihood -8803.024594, best rearrangement setting 12 Bootstrap[30]: Time 2.126140 seconds, bootstrap likelihood -8535.219094, best rearrangement setting 15 Bootstrap[31]: Time 2.734211 seconds, bootstrap likelihood -8826.677747, best rearrangement setting 15 Bootstrap[32]: Time 2.250171 seconds, bootstrap likelihood -7859.622688, best rearrangement setting 6 Bootstrap[33]: Time 2.577997 seconds, bootstrap likelihood -8715.562454, best rearrangement setting 15 Bootstrap[34]: Time 2.922166 seconds, bootstrap likelihood -8347.382432, best rearrangement setting 11 Bootstrap[35]: Time 2.798710 seconds, bootstrap likelihood -8771.694318, best rearrangement setting 8 Bootstrap[36]: Time 2.680464 seconds, bootstrap likelihood -9384.421788, best rearrangement setting 9 Bootstrap[37]: Time 2.755471 seconds, bootstrap likelihood -8007.472868, best rearrangement setting 11 Bootstrap[38]: Time 3.021755 seconds, bootstrap likelihood -8562.969860, best rearrangement setting 8 Bootstrap[39]: Time 2.645724 seconds, bootstrap likelihood -9319.472040, best rearrangement setting 13 Bootstrap[40]: Time 2.716608 seconds, bootstrap likelihood -9026.130278, best rearrangement setting 13 Bootstrap[41]: Time 2.497169 seconds, bootstrap likelihood -8331.329209, best rearrangement setting 10 Bootstrap[42]: Time 2.455973 seconds, bootstrap likelihood -8646.343415, best rearrangement setting 5 Bootstrap[43]: Time 2.644319 seconds, bootstrap likelihood -9157.875429, best rearrangement setting 14 Bootstrap[44]: Time 2.524247 seconds, bootstrap likelihood -8471.545393, best rearrangement setting 10 Bootstrap[45]: Time 3.007419 seconds, bootstrap likelihood -8802.775636, best rearrangement setting 15 Bootstrap[46]: Time 2.699500 seconds, bootstrap likelihood -8362.198592, best rearrangement setting 14 Bootstrap[47]: Time 2.802097 seconds, bootstrap likelihood -8938.635365, best rearrangement setting 8 Bootstrap[48]: Time 2.992740 seconds, bootstrap likelihood -7927.265409, best rearrangement setting 6 Bootstrap[49]: Time 2.651950 seconds, bootstrap likelihood -8601.891576, best rearrangement setting 7 Bootstrap[50]: Time 2.848852 seconds, bootstrap likelihood -8442.276404, best rearrangement setting 7 Bootstrap[51]: Time 3.036271 seconds, bootstrap likelihood -9149.230965, best rearrangement setting 11 Bootstrap[52]: Time 2.714788 seconds, bootstrap likelihood -7931.401437, best rearrangement setting 12 Bootstrap[53]: Time 2.361504 seconds, bootstrap likelihood -8853.909991, best rearrangement setting 8 Bootstrap[54]: Time 2.562915 seconds, bootstrap likelihood -8676.408846, best rearrangement setting 9 Bootstrap[55]: Time 2.668906 seconds, bootstrap likelihood -8420.298091, best rearrangement setting 11 Bootstrap[56]: Time 2.870105 seconds, bootstrap likelihood -8606.957319, best rearrangement setting 5 Bootstrap[57]: Time 3.040036 seconds, bootstrap likelihood -8628.959445, best rearrangement setting 7 Bootstrap[58]: Time 3.237010 seconds, bootstrap likelihood -8327.781509, best rearrangement setting 10 Bootstrap[59]: Time 2.705333 seconds, bootstrap likelihood -8489.784604, best rearrangement setting 9 Bootstrap[60]: Time 2.892230 seconds, bootstrap likelihood -8740.307830, best rearrangement setting 7 Bootstrap[61]: Time 2.822952 seconds, bootstrap likelihood -9205.096139, best rearrangement setting 5 Bootstrap[62]: Time 2.716801 seconds, bootstrap likelihood -8778.661830, best rearrangement setting 11 Bootstrap[63]: Time 2.406544 seconds, bootstrap likelihood -8660.241928, best rearrangement setting 12 Bootstrap[64]: Time 2.671600 seconds, bootstrap likelihood -9344.788796, best rearrangement setting 7 Bootstrap[65]: Time 2.873720 seconds, bootstrap likelihood -8629.498040, best rearrangement setting 5 Bootstrap[66]: Time 2.538994 seconds, bootstrap likelihood -8806.053039, best rearrangement setting 5 Bootstrap[67]: Time 2.830435 seconds, bootstrap likelihood -8264.759150, best rearrangement setting 15 Bootstrap[68]: Time 2.396368 seconds, bootstrap likelihood -8263.777541, best rearrangement setting 11 Bootstrap[69]: Time 2.536106 seconds, bootstrap likelihood -8620.209643, best rearrangement setting 5 Bootstrap[70]: Time 2.495144 seconds, bootstrap likelihood -8799.859406, best rearrangement setting 8 Bootstrap[71]: Time 2.906584 seconds, bootstrap likelihood -8180.444888, best rearrangement setting 10 Bootstrap[72]: Time 3.138186 seconds, bootstrap likelihood -9090.880716, best rearrangement setting 11 Bootstrap[73]: Time 2.956779 seconds, bootstrap likelihood -9151.279796, best rearrangement setting 9 Bootstrap[74]: Time 2.342207 seconds, bootstrap likelihood -8633.335910, best rearrangement setting 5 Bootstrap[75]: Time 2.904959 seconds, bootstrap likelihood -7739.920384, best rearrangement setting 8 Bootstrap[76]: Time 2.733269 seconds, bootstrap likelihood -8089.394648, best rearrangement setting 9 Bootstrap[77]: Time 2.351698 seconds, bootstrap likelihood -8079.011557, best rearrangement setting 11 Bootstrap[78]: Time 2.424916 seconds, bootstrap likelihood -7966.686928, best rearrangement setting 15 Bootstrap[79]: Time 2.857016 seconds, bootstrap likelihood -8080.708887, best rearrangement setting 9 Bootstrap[80]: Time 2.484948 seconds, bootstrap likelihood -8286.252952, best rearrangement setting 15 Bootstrap[81]: Time 3.076524 seconds, bootstrap likelihood -8769.248380, best rearrangement setting 7 Bootstrap[82]: Time 2.883968 seconds, bootstrap likelihood -8692.239244, best rearrangement setting 6 Bootstrap[83]: Time 2.479170 seconds, bootstrap likelihood -7699.379360, best rearrangement setting 10 Bootstrap[84]: Time 2.625243 seconds, bootstrap likelihood -8261.341959, best rearrangement setting 11 Bootstrap[85]: Time 2.683734 seconds, bootstrap likelihood -8553.912031, best rearrangement setting 8 Bootstrap[86]: Time 2.733593 seconds, bootstrap likelihood -8986.828572, best rearrangement setting 7 Bootstrap[87]: Time 2.848084 seconds, bootstrap likelihood -9129.711299, best rearrangement setting 7 Bootstrap[88]: Time 2.485447 seconds, bootstrap likelihood -8902.178410, best rearrangement setting 12 Bootstrap[89]: Time 2.495753 seconds, bootstrap likelihood -8551.096822, best rearrangement setting 10 Bootstrap[90]: Time 2.602619 seconds, bootstrap likelihood -8240.001289, best rearrangement setting 8 Bootstrap[91]: Time 2.848568 seconds, bootstrap likelihood -8573.213623, best rearrangement setting 12 Bootstrap[92]: Time 2.972128 seconds, bootstrap likelihood -8822.635189, best rearrangement setting 13 Bootstrap[93]: Time 2.512740 seconds, bootstrap likelihood -8001.448157, best rearrangement setting 15 Bootstrap[94]: Time 2.524322 seconds, bootstrap likelihood -8598.923408, best rearrangement setting 5 Bootstrap[95]: Time 2.592664 seconds, bootstrap likelihood -8836.732114, best rearrangement setting 5 Bootstrap[96]: Time 2.892493 seconds, bootstrap likelihood -8101.235153, best rearrangement setting 13 Bootstrap[97]: Time 2.529581 seconds, bootstrap likelihood -8196.950105, best rearrangement setting 11 Bootstrap[98]: Time 2.467491 seconds, bootstrap likelihood -8788.818443, best rearrangement setting 6 Bootstrap[99]: Time 2.713053 seconds, bootstrap likelihood -8779.081710, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 272.841793 seconds Average Time per Rapid Bootstrap 2.728418 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 239.772823 seconds Slow ML Search 0 Likelihood: -8565.363507 Slow ML Search 1 Likelihood: -8565.363507 Slow ML Search 2 Likelihood: -8565.363507 Slow ML Search 3 Likelihood: -8565.363507 Slow ML Search 4 Likelihood: -8565.363507 Slow ML Search 5 Likelihood: -8568.796027 Slow ML Search 6 Likelihood: -8568.796030 Slow ML Search 7 Likelihood: -8568.796065 Slow ML Search 8 Likelihood: -8568.796064 Slow ML Search 9 Likelihood: -8568.796064 Slow ML optimization finished Slow ML search Time: 86.188414 seconds Thorough ML search Time: 12.427007 seconds Final ML Optimization Likelihood: -8565.363696 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.611849 Tree-Length: 34.002986 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 338.559838 secs or 0.094044 hours Combined Bootstrap and ML search took 611.402483 secs or 0.169834 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.Symbiodinium-sp-Mp.MUSCLE Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Symbiodinium-sp-Mp.MUSCLE Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.Symbiodinium-sp-Mp.MUSCLE All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.Symbiodinium-sp-Mp.MUSCLE Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.Symbiodinium-sp-Mp.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.Symbiodinium-sp-Mp.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.Symbiodinium-sp-Mp.MUSCLE Overall execution time for full ML analysis: 611.415969 secs or 0.169838 hours or 0.007077 days