IMPORTANT WARNING: Alignment column 857 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Sequences Symbiodinium-sp-C15-CAMPEP_0192419642 and Symbiodinium-sp-C1-CAMPEP_0199632310 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-Wilson-CAMPEP_0189447594 and Karenia-brevis-SP3-CAMPEP_0189295442 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-CCMP2229-CAMPEP_0188881724 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-SP1-CAMPEP_0189089362 and Karenia-brevis-CCMP2229-CAMPEP_0188985338 are exactly identical IMPORTANT WARNING: Sequences Chromera-velia-CCMP2878_CAMPEP_0184618748 and Chromera-velia-CAMPEP_0184618748 are exactly identical IMPORTANT WARNING: Sequences Thalassiosira-weissflogii-CCMP1336_CAMPEP_0193075034 and Thalassiosira-weissflogii-CCMP1336_CAMPEP_0193074504 are exactly identical IMPORTANT WARNING: Sequences Thalassiosira-weissflogii-CCMP1336_CAMPEP_0193075034 and Kryptoperidinium-foliaceum-CAMPEP_0189626928 are exactly identical IMPORTANT WARNING: Sequences Thalassiosira-weissflogii-CCMP1336_CAMPEP_0193075034 and Glenodinium-foliaceum-CAMPEP_0188362332 are exactly identical IMPORTANT WARNING: Sequences Thalassiosira-weissflogii-CCMP1336_CAMPEP_0193075034 and Durinskia-baltica-CAMPEP_0199915030 are exactly identical IMPORTANT WARNING: Sequences Gloeochaete-witrockiana-SAG46_84_CAMPEP_0193997864 and Gloeochaete-witrockiana-SAG46_84_CAMPEP_0194019796 are exactly identical IMPORTANT WARNING: Sequences Fibrocapsa-japonica-CCMP1661_CAMPEP_0113937756 and Fibrocapsa-japonica-CCMP1661_CAMPEP_0113938028 are exactly identical IMPORTANT WARNING: Sequences Lotharella-globosa-CCCM811_CAMPEP_0190151100 and Vaucheria-litorea-CCMP2940_CAMPEP_0199159788 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 Found 16 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. IMPORTANT WARNING Found 1 column that contains only undetermined values which will be treated as missing data. Normally these columns should be excluded from the analysis. Just in case you might need it, an alignment file with sequence duplicates and undetermined columns removed is printed to file H4-with-other-lineages.muscle.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 584 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 86.30% 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: 584 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.fa -n RAxML-H4-with-other-lineages.muscle -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.613483 Bootstrap[0]: Time 10.424473 seconds, bootstrap likelihood -10517.555218, best rearrangement setting 13 Bootstrap[1]: Time 9.003456 seconds, bootstrap likelihood -11139.874752, best rearrangement setting 13 Bootstrap[2]: Time 7.473961 seconds, bootstrap likelihood -11051.852997, best rearrangement setting 12 Bootstrap[3]: Time 8.270555 seconds, bootstrap likelihood -10719.122444, best rearrangement setting 15 Bootstrap[4]: Time 7.335587 seconds, bootstrap likelihood -11244.181513, best rearrangement setting 10 Bootstrap[5]: Time 7.284971 seconds, bootstrap likelihood -10835.514219, best rearrangement setting 10 Bootstrap[6]: Time 9.314602 seconds, bootstrap likelihood -10755.328231, best rearrangement setting 6 Bootstrap[7]: Time 10.251599 seconds, bootstrap likelihood -11281.081079, best rearrangement setting 14 Bootstrap[8]: Time 6.856086 seconds, bootstrap likelihood -9963.977366, best rearrangement setting 5 Bootstrap[9]: Time 7.222967 seconds, bootstrap likelihood -10929.011786, best rearrangement setting 7 Bootstrap[10]: Time 8.587920 seconds, bootstrap likelihood -10686.068710, best rearrangement setting 7 Bootstrap[11]: Time 7.334211 seconds, bootstrap likelihood -9736.308977, best rearrangement setting 5 Bootstrap[12]: Time 8.985312 seconds, bootstrap likelihood -10437.066561, best rearrangement setting 8 Bootstrap[13]: Time 8.967102 seconds, bootstrap likelihood -9913.628908, best rearrangement setting 7 Bootstrap[14]: Time 9.290770 seconds, bootstrap likelihood -10076.607952, best rearrangement setting 12 Bootstrap[15]: Time 7.439907 seconds, bootstrap likelihood -10797.927536, best rearrangement setting 15 Bootstrap[16]: Time 8.372045 seconds, bootstrap likelihood -11231.538988, best rearrangement setting 12 Bootstrap[17]: Time 8.383978 seconds, bootstrap likelihood -10256.198961, best rearrangement setting 12 Bootstrap[18]: Time 6.449530 seconds, bootstrap likelihood -10332.714304, best rearrangement setting 5 Bootstrap[19]: Time 8.169635 seconds, bootstrap likelihood -10500.824725, best rearrangement setting 8 Bootstrap[20]: Time 7.959141 seconds, bootstrap likelihood -10942.336705, best rearrangement setting 10 Bootstrap[21]: Time 7.586570 seconds, bootstrap likelihood -10452.051228, best rearrangement setting 6 Bootstrap[22]: Time 6.981010 seconds, bootstrap likelihood -10986.001674, best rearrangement setting 5 Bootstrap[23]: Time 7.306142 seconds, bootstrap likelihood -10759.423771, best rearrangement setting 7 Bootstrap[24]: Time 8.707547 seconds, bootstrap likelihood -10733.170878, best rearrangement setting 8 Bootstrap[25]: Time 8.098862 seconds, bootstrap likelihood -11003.400843, best rearrangement setting 6 Bootstrap[26]: Time 9.156028 seconds, bootstrap likelihood -11753.046196, best rearrangement setting 12 Bootstrap[27]: Time 8.728785 seconds, bootstrap likelihood -10306.575179, best rearrangement setting 10 Bootstrap[28]: Time 9.035943 seconds, bootstrap likelihood -10747.070960, best rearrangement setting 11 Bootstrap[29]: Time 7.967471 seconds, bootstrap likelihood -10589.202688, best rearrangement setting 12 Bootstrap[30]: Time 8.041346 seconds, bootstrap likelihood -10279.165371, best rearrangement setting 15 Bootstrap[31]: Time 8.590941 seconds, bootstrap likelihood -10698.049683, best rearrangement setting 15 Bootstrap[32]: Time 7.905722 seconds, bootstrap likelihood -10551.723032, best rearrangement setting 6 Bootstrap[33]: Time 7.342297 seconds, bootstrap likelihood -11193.890605, best rearrangement setting 15 Bootstrap[34]: Time 11.213720 seconds, bootstrap likelihood -10218.061667, best rearrangement setting 11 Bootstrap[35]: Time 8.574471 seconds, bootstrap likelihood -10579.862400, best rearrangement setting 8 Bootstrap[36]: Time 8.202422 seconds, bootstrap likelihood -10733.775367, best rearrangement setting 9 Bootstrap[37]: Time 7.777754 seconds, bootstrap likelihood -10098.901425, best rearrangement setting 11 Bootstrap[38]: Time 8.440636 seconds, bootstrap likelihood -11026.545510, best rearrangement setting 8 Bootstrap[39]: Time 8.087788 seconds, bootstrap likelihood -10567.986930, best rearrangement setting 13 Bootstrap[40]: Time 8.245139 seconds, bootstrap likelihood -10885.448911, best rearrangement setting 13 Bootstrap[41]: Time 7.837435 seconds, bootstrap likelihood -11375.447778, best rearrangement setting 10 Bootstrap[42]: Time 8.401613 seconds, bootstrap likelihood -10823.596827, best rearrangement setting 5 Bootstrap[43]: Time 9.076458 seconds, bootstrap likelihood -12255.739828, best rearrangement setting 14 Bootstrap[44]: Time 8.483886 seconds, bootstrap likelihood -9710.907753, best rearrangement setting 10 Bootstrap[45]: Time 9.966039 seconds, bootstrap likelihood -11365.159826, best rearrangement setting 15 Bootstrap[46]: Time 9.906815 seconds, bootstrap likelihood -10545.711089, best rearrangement setting 14 Bootstrap[47]: Time 7.927661 seconds, bootstrap likelihood -10267.957877, best rearrangement setting 8 Bootstrap[48]: Time 8.765718 seconds, bootstrap likelihood -10984.918621, best rearrangement setting 6 Bootstrap[49]: Time 8.016612 seconds, bootstrap likelihood -9678.611200, best rearrangement setting 7 Bootstrap[50]: Time 8.031058 seconds, bootstrap likelihood -10434.184222, best rearrangement setting 7 Bootstrap[51]: Time 7.653279 seconds, bootstrap likelihood -9918.235173, best rearrangement setting 11 Bootstrap[52]: Time 9.258062 seconds, bootstrap likelihood -10196.340047, best rearrangement setting 12 Bootstrap[53]: Time 9.004068 seconds, bootstrap likelihood -11210.861041, best rearrangement setting 8 Bootstrap[54]: Time 7.988705 seconds, bootstrap likelihood -10250.449876, best rearrangement setting 9 Bootstrap[55]: Time 9.537961 seconds, bootstrap likelihood -9813.143545, best rearrangement setting 11 Bootstrap[56]: Time 7.457016 seconds, bootstrap likelihood -10273.389047, best rearrangement setting 5 Bootstrap[57]: Time 8.164670 seconds, bootstrap likelihood -10654.637943, best rearrangement setting 7 Bootstrap[58]: Time 9.566517 seconds, bootstrap likelihood -10937.467837, best rearrangement setting 10 Bootstrap[59]: Time 8.083999 seconds, bootstrap likelihood -10405.257630, best rearrangement setting 9 Bootstrap[60]: Time 7.548814 seconds, bootstrap likelihood -10887.688957, best rearrangement setting 7 Bootstrap[61]: Time 6.860741 seconds, bootstrap likelihood -10295.958305, best rearrangement setting 5 Bootstrap[62]: Time 9.165893 seconds, bootstrap likelihood -10876.952896, best rearrangement setting 11 Bootstrap[63]: Time 7.132220 seconds, bootstrap likelihood -10426.071081, best rearrangement setting 12 Bootstrap[64]: Time 7.391469 seconds, bootstrap likelihood -10223.466519, best rearrangement setting 7 Bootstrap[65]: Time 6.941572 seconds, bootstrap likelihood -10958.234188, best rearrangement setting 5 Bootstrap[66]: Time 8.618341 seconds, bootstrap likelihood -11235.157075, best rearrangement setting 5 Bootstrap[67]: Time 10.449772 seconds, bootstrap likelihood -10193.959408, best rearrangement setting 15 Bootstrap[68]: Time 9.513925 seconds, bootstrap likelihood -10626.494409, best rearrangement setting 11 Bootstrap[69]: Time 7.191102 seconds, bootstrap likelihood -10771.956811, best rearrangement setting 5 Bootstrap[70]: Time 7.779444 seconds, bootstrap likelihood -11275.814314, best rearrangement setting 8 Bootstrap[71]: Time 8.299744 seconds, bootstrap likelihood -10199.074659, best rearrangement setting 10 Bootstrap[72]: Time 8.968032 seconds, bootstrap likelihood -10591.168004, best rearrangement setting 11 Bootstrap[73]: Time 8.153465 seconds, bootstrap likelihood -11372.643500, best rearrangement setting 9 Bootstrap[74]: Time 8.175783 seconds, bootstrap likelihood -10130.445660, best rearrangement setting 5 Bootstrap[75]: Time 7.716254 seconds, bootstrap likelihood -9900.999959, best rearrangement setting 8 Bootstrap[76]: Time 9.342551 seconds, bootstrap likelihood -9967.235492, best rearrangement setting 9 Bootstrap[77]: Time 8.307452 seconds, bootstrap likelihood -10473.171201, best rearrangement setting 11 Bootstrap[78]: Time 10.510632 seconds, bootstrap likelihood -11456.625477, best rearrangement setting 15 Bootstrap[79]: Time 8.494327 seconds, bootstrap likelihood -9568.310683, best rearrangement setting 9 Bootstrap[80]: Time 7.543812 seconds, bootstrap likelihood -10561.278737, best rearrangement setting 15 Bootstrap[81]: Time 7.438431 seconds, bootstrap likelihood -11443.802207, best rearrangement setting 7 Bootstrap[82]: Time 7.874058 seconds, bootstrap likelihood -10444.336687, best rearrangement setting 6 Bootstrap[83]: Time 8.020379 seconds, bootstrap likelihood -10938.688937, best rearrangement setting 10 Bootstrap[84]: Time 8.410336 seconds, bootstrap likelihood -10156.209458, best rearrangement setting 11 Bootstrap[85]: Time 8.419809 seconds, bootstrap likelihood -10836.346198, best rearrangement setting 8 Bootstrap[86]: Time 8.083803 seconds, bootstrap likelihood -10983.355755, best rearrangement setting 7 Bootstrap[87]: Time 8.308666 seconds, bootstrap likelihood -10884.476529, best rearrangement setting 7 Bootstrap[88]: Time 9.310108 seconds, bootstrap likelihood -10745.392087, best rearrangement setting 12 Bootstrap[89]: Time 8.206486 seconds, bootstrap likelihood -11468.461858, best rearrangement setting 10 Bootstrap[90]: Time 7.454377 seconds, bootstrap likelihood -9854.165581, best rearrangement setting 8 Bootstrap[91]: Time 10.685487 seconds, bootstrap likelihood -10563.270645, best rearrangement setting 12 Bootstrap[92]: Time 7.485730 seconds, bootstrap likelihood -10758.225023, best rearrangement setting 13 Bootstrap[93]: Time 8.213968 seconds, bootstrap likelihood -10325.006485, best rearrangement setting 15 Bootstrap[94]: Time 7.588789 seconds, bootstrap likelihood -10303.461028, best rearrangement setting 5 Bootstrap[95]: Time 6.855762 seconds, bootstrap likelihood -10986.600090, best rearrangement setting 5 Bootstrap[96]: Time 8.414512 seconds, bootstrap likelihood -10142.475863, best rearrangement setting 13 Bootstrap[97]: Time 6.967629 seconds, bootstrap likelihood -10883.167629, best rearrangement setting 11 Bootstrap[98]: Time 6.219776 seconds, bootstrap likelihood -10503.956225, best rearrangement setting 6 Bootstrap[99]: Time 10.320920 seconds, bootstrap likelihood -10306.369719, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 831.016942 seconds Average Time per Rapid Bootstrap 8.310169 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 851.338999 seconds Slow ML Search 0 Likelihood: -10695.947170 Slow ML Search 1 Likelihood: -10696.371171 Slow ML Search 2 Likelihood: -10696.898693 Slow ML Search 3 Likelihood: -10698.078227 Slow ML Search 4 Likelihood: -10697.813482 Slow ML Search 5 Likelihood: -10696.386836 Slow ML Search 6 Likelihood: -10695.046171 Slow ML Search 7 Likelihood: -10696.399878 Slow ML Search 8 Likelihood: -10698.916910 Slow ML Search 9 Likelihood: -10698.131450 Slow ML optimization finished Slow ML search Time: 517.058653 seconds Thorough ML search Time: 25.070638 seconds Final ML Optimization Likelihood: -10695.067060 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.665407 Tree-Length: 74.211375 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 1393.578342 secs or 0.387105 hours Combined Bootstrap and ML search took 2224.596109 secs or 0.617943 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 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 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 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 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 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 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 Overall execution time for full ML analysis: 2224.647170 secs or 0.617958 hours or 0.025748 days