IMPORTANT WARNING: Sequences Gloeochaete-witrockiana-SAG46_84_CAMPEP_0194019796 and Gloeochaete-witrockiana-SAG46_84_CAMPEP_0193997864 are exactly identical IMPORTANT WARNING: Sequences Vaucheria-litorea-CCMP2940_CAMPEP_0199159788 and Lotharella-globosa-CCCM811_CAMPEP_0190151100 are exactly identical IMPORTANT WARNING: Sequences Bigelowiella-natans-CCMP623_CAMPEP_0169542970 and Bigelowiella-natans-CCMP623_CAMPEP_0169558516 are exactly identical IMPORTANT WARNING: Sequences Prymnesium-parvum-Texoma1_CAMPEP_0191267362 and Prymnesium-parvum-Texoma1_CAMPEP_0191265826 are exactly identical IMPORTANT WARNING: Sequences Prymnesium-parvum-Texoma1_CAMPEP_0191267362 and Emiliania-huxleyi-374_CAMPEP_0187594326 are exactly identical IMPORTANT WARNING: Sequences Fibrocapsa-japonica-CCMP1661_CAMPEP_0113938028 and Fibrocapsa-japonica-CCMP1661_CAMPEP_0113937756 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-CCMP2229-CAMPEP_0188985338 and Karenia-brevis-SP1-CAMPEP_0189089362 are exactly identical IMPORTANT WARNING: Sequences Kryptoperidinium-foliaceum-CAMPEP_0189626928 and Thalassiosira-weissflogii-CCMP1336_CAMPEP_0193075034 are exactly identical IMPORTANT WARNING: Sequences Kryptoperidinium-foliaceum-CAMPEP_0189626928 and Glenodinium-foliaceum-CAMPEP_0188362332 are exactly identical IMPORTANT WARNING: Sequences Kryptoperidinium-foliaceum-CAMPEP_0189626928 and Thalassiosira-weissflogii-CCMP1336_CAMPEP_0193074504 are exactly identical IMPORTANT WARNING: Sequences Kryptoperidinium-foliaceum-CAMPEP_0189626928 and Durinskia-baltica-CAMPEP_0199915030 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-Wilson-CAMPEP_0189447594 and Karenia-brevis-CCMP2229-CAMPEP_0188881724 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-Wilson-CAMPEP_0189447594 and Karenia-brevis-SP1-CAMPEP_0189018818 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-Wilson-CAMPEP_0189447594 and Karenia-brevis-SP3-CAMPEP_0189295442 are exactly identical IMPORTANT WARNING: Sequences Symbiodinium-sp-C1-CAMPEP_0199632310 and Symbiodinium-sp-C15-CAMPEP_0192419642 are exactly identical IMPORTANT WARNING: Sequences Chromera-velia-CCMP2878_CAMPEP_0184618748 and Chromera-velia-CAMPEP_0184618748 are exactly identical IMPORTANT WARNING: Sequences Amoebophrya-sp.-CAMPEP_0178991388 and Amoebophrya-sp.-CAMPEP_0179001278 are exactly identical IMPORTANT WARNING Found 17 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 H4-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 100 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 1.26% 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: 100 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s H4-with-other-lineages.muscle.minCov50.fa -n RAxML-H4-with-other-lineages.muscle.minCov50 -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.111631 Bootstrap[0]: Time 3.380591 seconds, bootstrap likelihood -3931.728517, best rearrangement setting 13 Bootstrap[1]: Time 2.880171 seconds, bootstrap likelihood -4291.697974, best rearrangement setting 13 Bootstrap[2]: Time 2.974119 seconds, bootstrap likelihood -3638.477616, best rearrangement setting 12 Bootstrap[3]: Time 2.915065 seconds, bootstrap likelihood -3804.928819, best rearrangement setting 15 Bootstrap[4]: Time 3.495463 seconds, bootstrap likelihood -4001.796194, best rearrangement setting 10 Bootstrap[5]: Time 2.759272 seconds, bootstrap likelihood -3951.950594, best rearrangement setting 10 Bootstrap[6]: Time 3.034621 seconds, bootstrap likelihood -4172.711060, best rearrangement setting 6 Bootstrap[7]: Time 2.761252 seconds, bootstrap likelihood -4113.680434, best rearrangement setting 14 Bootstrap[8]: Time 2.786008 seconds, bootstrap likelihood -3832.106641, best rearrangement setting 5 Bootstrap[9]: Time 2.957249 seconds, bootstrap likelihood -3661.206343, best rearrangement setting 7 Bootstrap[10]: Time 3.157799 seconds, bootstrap likelihood -3378.936455, best rearrangement setting 7 Bootstrap[11]: Time 2.802509 seconds, bootstrap likelihood -3453.712730, best rearrangement setting 5 Bootstrap[12]: Time 3.455739 seconds, bootstrap likelihood -3487.693118, best rearrangement setting 8 Bootstrap[13]: Time 3.008145 seconds, bootstrap likelihood -3934.001480, best rearrangement setting 7 Bootstrap[14]: Time 3.011525 seconds, bootstrap likelihood -4423.753907, best rearrangement setting 12 Bootstrap[15]: Time 3.607533 seconds, bootstrap likelihood -3924.156875, best rearrangement setting 15 Bootstrap[16]: Time 3.286562 seconds, bootstrap likelihood -3757.072569, best rearrangement setting 12 Bootstrap[17]: Time 3.297403 seconds, bootstrap likelihood -3705.477694, best rearrangement setting 12 Bootstrap[18]: Time 3.007832 seconds, bootstrap likelihood -3830.783558, best rearrangement setting 5 Bootstrap[19]: Time 3.284035 seconds, bootstrap likelihood -3726.727263, best rearrangement setting 8 Bootstrap[20]: Time 2.846953 seconds, bootstrap likelihood -3770.022259, best rearrangement setting 10 Bootstrap[21]: Time 2.641764 seconds, bootstrap likelihood -3757.645167, best rearrangement setting 6 Bootstrap[22]: Time 3.007041 seconds, bootstrap likelihood -3856.401076, best rearrangement setting 5 Bootstrap[23]: Time 2.663965 seconds, bootstrap likelihood -3486.221646, best rearrangement setting 7 Bootstrap[24]: Time 2.911915 seconds, bootstrap likelihood -3609.215811, best rearrangement setting 8 Bootstrap[25]: Time 2.850467 seconds, bootstrap likelihood -3294.675061, best rearrangement setting 6 Bootstrap[26]: Time 2.481708 seconds, bootstrap likelihood -4249.031670, best rearrangement setting 12 Bootstrap[27]: Time 3.769867 seconds, bootstrap likelihood -3653.598401, best rearrangement setting 10 Bootstrap[28]: Time 2.983636 seconds, bootstrap likelihood -4162.421795, best rearrangement setting 11 Bootstrap[29]: Time 3.146916 seconds, bootstrap likelihood -3530.782460, best rearrangement setting 12 Bootstrap[30]: Time 2.727113 seconds, bootstrap likelihood -3940.780184, best rearrangement setting 15 Bootstrap[31]: Time 3.956312 seconds, bootstrap likelihood -3308.785594, best rearrangement setting 15 Bootstrap[32]: Time 3.159529 seconds, bootstrap likelihood -3812.900351, best rearrangement setting 6 Bootstrap[33]: Time 3.073656 seconds, bootstrap likelihood -3903.196428, best rearrangement setting 15 Bootstrap[34]: Time 2.826640 seconds, bootstrap likelihood -4040.116526, best rearrangement setting 11 Bootstrap[35]: Time 2.755636 seconds, bootstrap likelihood -3887.114938, best rearrangement setting 8 Bootstrap[36]: Time 2.816536 seconds, bootstrap likelihood -3760.270713, best rearrangement setting 9 Bootstrap[37]: Time 2.793705 seconds, bootstrap likelihood -4167.232076, best rearrangement setting 11 Bootstrap[38]: Time 3.117105 seconds, bootstrap likelihood -3910.496385, best rearrangement setting 8 Bootstrap[39]: Time 3.615313 seconds, bootstrap likelihood -3748.432563, best rearrangement setting 13 Bootstrap[40]: Time 3.684937 seconds, bootstrap likelihood -3890.196553, best rearrangement setting 13 Bootstrap[41]: Time 3.262675 seconds, bootstrap likelihood -4119.324238, best rearrangement setting 10 Bootstrap[42]: Time 2.911191 seconds, bootstrap likelihood -4413.856696, best rearrangement setting 5 Bootstrap[43]: Time 3.122150 seconds, bootstrap likelihood -3998.398173, best rearrangement setting 14 Bootstrap[44]: Time 2.975719 seconds, bootstrap likelihood -3738.837938, best rearrangement setting 10 Bootstrap[45]: Time 3.777477 seconds, bootstrap likelihood -3793.913386, best rearrangement setting 15 Bootstrap[46]: Time 2.918304 seconds, bootstrap likelihood -3684.401382, best rearrangement setting 14 Bootstrap[47]: Time 2.672124 seconds, bootstrap likelihood -3925.911958, best rearrangement setting 8 Bootstrap[48]: Time 2.772783 seconds, bootstrap likelihood -3929.346271, best rearrangement setting 6 Bootstrap[49]: Time 2.822627 seconds, bootstrap likelihood -3892.187503, best rearrangement setting 7 Bootstrap[50]: Time 3.002168 seconds, bootstrap likelihood -3823.405670, best rearrangement setting 7 Bootstrap[51]: Time 3.093684 seconds, bootstrap likelihood -3708.528159, best rearrangement setting 11 Bootstrap[52]: Time 3.252805 seconds, bootstrap likelihood -3661.656551, best rearrangement setting 12 Bootstrap[53]: Time 3.064815 seconds, bootstrap likelihood -3656.479758, best rearrangement setting 8 Bootstrap[54]: Time 3.061666 seconds, bootstrap likelihood -3674.271918, best rearrangement setting 9 Bootstrap[55]: Time 2.683104 seconds, bootstrap likelihood -4229.840161, best rearrangement setting 11 Bootstrap[56]: Time 2.652896 seconds, bootstrap likelihood -4068.581579, best rearrangement setting 5 Bootstrap[57]: Time 2.668024 seconds, bootstrap likelihood -3814.321715, best rearrangement setting 7 Bootstrap[58]: Time 2.868820 seconds, bootstrap likelihood -3500.324821, best rearrangement setting 10 Bootstrap[59]: Time 2.878598 seconds, bootstrap likelihood -3757.670293, best rearrangement setting 9 Bootstrap[60]: Time 2.717032 seconds, bootstrap likelihood -4016.372948, best rearrangement setting 7 Bootstrap[61]: Time 3.186183 seconds, bootstrap likelihood -3919.640619, best rearrangement setting 5 Bootstrap[62]: Time 3.001761 seconds, bootstrap likelihood -3878.935878, best rearrangement setting 11 Bootstrap[63]: Time 3.185516 seconds, bootstrap likelihood -3889.051034, best rearrangement setting 12 Bootstrap[64]: Time 3.120149 seconds, bootstrap likelihood -3708.418050, best rearrangement setting 7 Bootstrap[65]: Time 2.720090 seconds, bootstrap likelihood -4012.780485, best rearrangement setting 5 Bootstrap[66]: Time 3.000434 seconds, bootstrap likelihood -3546.042346, best rearrangement setting 5 Bootstrap[67]: Time 2.954399 seconds, bootstrap likelihood -3874.343091, best rearrangement setting 15 Bootstrap[68]: Time 2.940551 seconds, bootstrap likelihood -3826.849053, best rearrangement setting 11 Bootstrap[69]: Time 2.784898 seconds, bootstrap likelihood -4056.772425, best rearrangement setting 5 Bootstrap[70]: Time 3.391689 seconds, bootstrap likelihood -3663.933827, best rearrangement setting 8 Bootstrap[71]: Time 2.914428 seconds, bootstrap likelihood -3690.881063, best rearrangement setting 10 Bootstrap[72]: Time 3.041194 seconds, bootstrap likelihood -3816.654789, best rearrangement setting 11 Bootstrap[73]: Time 2.801898 seconds, bootstrap likelihood -4008.365134, best rearrangement setting 9 Bootstrap[74]: Time 2.675945 seconds, bootstrap likelihood -3999.925798, best rearrangement setting 5 Bootstrap[75]: Time 2.835076 seconds, bootstrap likelihood -3933.903200, best rearrangement setting 8 Bootstrap[76]: Time 2.958300 seconds, bootstrap likelihood -3507.301325, best rearrangement setting 9 Bootstrap[77]: Time 4.657609 seconds, bootstrap likelihood -4073.174474, best rearrangement setting 11 Bootstrap[78]: Time 3.156514 seconds, bootstrap likelihood -3559.546130, best rearrangement setting 15 Bootstrap[79]: Time 2.991117 seconds, bootstrap likelihood -3794.840131, best rearrangement setting 9 Bootstrap[80]: Time 2.981498 seconds, bootstrap likelihood -3621.086713, best rearrangement setting 15 Bootstrap[81]: Time 2.838216 seconds, bootstrap likelihood -3492.264778, best rearrangement setting 7 Bootstrap[82]: Time 2.750314 seconds, bootstrap likelihood -3829.578261, best rearrangement setting 6 Bootstrap[83]: Time 3.237347 seconds, bootstrap likelihood -3499.460599, best rearrangement setting 10 Bootstrap[84]: Time 3.120590 seconds, bootstrap likelihood -3420.134201, best rearrangement setting 11 Bootstrap[85]: Time 3.214649 seconds, bootstrap likelihood -3385.127723, best rearrangement setting 8 Bootstrap[86]: Time 2.746979 seconds, bootstrap likelihood -3894.137212, best rearrangement setting 7 Bootstrap[87]: Time 2.694643 seconds, bootstrap likelihood -3711.976202, best rearrangement setting 7 Bootstrap[88]: Time 3.468918 seconds, bootstrap likelihood -3815.062638, best rearrangement setting 12 Bootstrap[89]: Time 3.931891 seconds, bootstrap likelihood -3965.401803, best rearrangement setting 10 Bootstrap[90]: Time 2.860668 seconds, bootstrap likelihood -3898.411600, best rearrangement setting 8 Bootstrap[91]: Time 2.898882 seconds, bootstrap likelihood -4305.420809, best rearrangement setting 12 Bootstrap[92]: Time 2.865078 seconds, bootstrap likelihood -3690.985053, best rearrangement setting 13 Bootstrap[93]: Time 3.055865 seconds, bootstrap likelihood -3977.882595, best rearrangement setting 15 Bootstrap[94]: Time 2.781955 seconds, bootstrap likelihood -3731.604676, best rearrangement setting 5 Bootstrap[95]: Time 2.796875 seconds, bootstrap likelihood -3840.306108, best rearrangement setting 5 Bootstrap[96]: Time 3.276301 seconds, bootstrap likelihood -3681.816813, best rearrangement setting 13 Bootstrap[97]: Time 2.973497 seconds, bootstrap likelihood -4021.446026, best rearrangement setting 11 Bootstrap[98]: Time 2.655954 seconds, bootstrap likelihood -3515.535631, best rearrangement setting 6 Bootstrap[99]: Time 3.128641 seconds, bootstrap likelihood -4038.698161, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 303.697280 seconds Average Time per Rapid Bootstrap 3.036973 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 274.418996 seconds Slow ML Search 0 Likelihood: -3965.896468 Slow ML Search 1 Likelihood: -3965.896476 Slow ML Search 2 Likelihood: -3966.788573 Slow ML Search 3 Likelihood: -3965.092377 Slow ML Search 4 Likelihood: -3965.896376 Slow ML Search 5 Likelihood: -3965.092457 Slow ML Search 6 Likelihood: -3968.632153 Slow ML Search 7 Likelihood: -3965.896317 Slow ML Search 8 Likelihood: -3969.647179 Slow ML Search 9 Likelihood: -3965.896364 Slow ML optimization finished Slow ML search Time: 159.910545 seconds Thorough ML search Time: 9.536176 seconds Final ML Optimization Likelihood: -3965.080447 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.049372 Tree-Length: 12.603224 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 443.961672 secs or 0.123323 hours Combined Bootstrap and ML search took 747.660330 secs or 0.207683 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-H4-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-H4-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-H4-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-H4-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-H4-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-H4-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-H4-with-other-lineages.muscle.minCov50 Overall execution time for full ML analysis: 747.688592 secs or 0.207691 hours or 0.008654 days