IMPORTANT WARNING: Sequences P_sexaurelia-Sample_127_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_130_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_127_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_134_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_128_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_tetraurelia-Sample_291_60aa-ORF_renamed_min100aa_ORF and P_tetraurelia-Sample_99_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_tetraurelia-Sample_291_60aa-ORF_renamed_min100aa_ORF and P_tetraurelia-Sample_A_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING Found 5 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 Ymf65.renamed.muscle.Oligohymenophorea.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 395 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 21.73% 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: 395 Name: No Name Provided DataType: AA Substitution Matrix: GTR Using empirical base frequencies RAxML was called as follows: raxml -f a -s Ymf65.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 195.337469 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 16.820867 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.041538 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Time for BS model parameter optimization 20.725422 Bootstrap[0]: Time 22.405139 seconds, bootstrap likelihood -6064.345632, best rearrangement setting 13 Bootstrap[1]: Time 1.444492 seconds, bootstrap likelihood -6141.802749, best rearrangement setting 13 Bootstrap[2]: Time 1.801057 seconds, bootstrap likelihood -5740.136877, best rearrangement setting 12 Bootstrap[3]: Time 0.537569 seconds, bootstrap likelihood -6150.695616, best rearrangement setting 15 Bootstrap[4]: Time 1.361518 seconds, bootstrap likelihood -6031.416249, best rearrangement setting 10 Bootstrap[5]: Time 1.586193 seconds, bootstrap likelihood -5918.985410, best rearrangement setting 10 Bootstrap[6]: Time 1.682263 seconds, bootstrap likelihood -6227.948305, best rearrangement setting 6 Bootstrap[7]: Time 1.402012 seconds, bootstrap likelihood -5925.414823, best rearrangement setting 14 Bootstrap[8]: Time 1.546228 seconds, bootstrap likelihood -6162.052064, best rearrangement setting 5 Bootstrap[9]: Time 1.844969 seconds, bootstrap likelihood -5975.312185, best rearrangement setting 7 Bootstrap[10]: Time 1.700876 seconds, bootstrap likelihood -6374.144507, best rearrangement setting 7 Bootstrap[11]: Time 1.397230 seconds, bootstrap likelihood -6091.904781, best rearrangement setting 5 Bootstrap[12]: Time 1.477799 seconds, bootstrap likelihood -5945.214272, best rearrangement setting 8 Bootstrap[13]: Time 1.767452 seconds, bootstrap likelihood -6356.551185, best rearrangement setting 7 Bootstrap[14]: Time 1.568921 seconds, bootstrap likelihood -5882.600461, best rearrangement setting 12 Bootstrap[15]: Time 1.819310 seconds, bootstrap likelihood -6178.170698, best rearrangement setting 15 Bootstrap[16]: Time 1.897014 seconds, bootstrap likelihood -6189.336583, best rearrangement setting 12 Bootstrap[17]: Time 1.642853 seconds, bootstrap likelihood -5902.029565, best rearrangement setting 12 Bootstrap[18]: Time 1.596800 seconds, bootstrap likelihood -6169.209132, best rearrangement setting 5 Bootstrap[19]: Time 1.887675 seconds, bootstrap likelihood -6080.636129, best rearrangement setting 8 Bootstrap[20]: Time 1.417191 seconds, bootstrap likelihood -5973.556498, best rearrangement setting 10 Bootstrap[21]: Time 1.528897 seconds, bootstrap likelihood -5974.733756, best rearrangement setting 6 Bootstrap[22]: Time 1.771466 seconds, bootstrap likelihood -5828.247365, best rearrangement setting 5 Bootstrap[23]: Time 1.411833 seconds, bootstrap likelihood -6122.480526, best rearrangement setting 7 Bootstrap[24]: Time 1.629625 seconds, bootstrap likelihood -5874.085026, best rearrangement setting 8 Bootstrap[25]: Time 1.749811 seconds, bootstrap likelihood -5986.836911, best rearrangement setting 6 Bootstrap[26]: Time 1.456219 seconds, bootstrap likelihood -6021.881670, best rearrangement setting 12 Bootstrap[27]: Time 0.540803 seconds, bootstrap likelihood -6130.317732, best rearrangement setting 10 Bootstrap[28]: Time 1.552179 seconds, bootstrap likelihood -6178.446829, best rearrangement setting 11 Bootstrap[29]: Time 1.452275 seconds, bootstrap likelihood -6087.414591, best rearrangement setting 12 Bootstrap[30]: Time 1.484376 seconds, bootstrap likelihood -6186.779726, best rearrangement setting 15 Bootstrap[31]: Time 1.478871 seconds, bootstrap likelihood -6078.090863, best rearrangement setting 15 Bootstrap[32]: Time 1.569769 seconds, bootstrap likelihood -6157.312521, best rearrangement setting 6 Bootstrap[33]: Time 1.479474 seconds, bootstrap likelihood -6096.320469, best rearrangement setting 15 Bootstrap[34]: Time 1.557825 seconds, bootstrap likelihood -6419.106952, best rearrangement setting 11 Bootstrap[35]: Time 1.717994 seconds, bootstrap likelihood -5944.901175, best rearrangement setting 8 Bootstrap[36]: Time 1.711513 seconds, bootstrap likelihood -6177.439861, best rearrangement setting 9 Bootstrap[37]: Time 1.590863 seconds, bootstrap likelihood -5734.577438, best rearrangement setting 11 Bootstrap[38]: Time 1.541244 seconds, bootstrap likelihood -5937.475179, best rearrangement setting 8 Bootstrap[39]: Time 1.393892 seconds, bootstrap likelihood -6056.866863, best rearrangement setting 13 Bootstrap[40]: Time 1.671802 seconds, bootstrap likelihood -5978.990229, best rearrangement setting 13 Bootstrap[41]: Time 1.367569 seconds, bootstrap likelihood -5861.677356, best rearrangement setting 10 Bootstrap[42]: Time 1.479086 seconds, bootstrap likelihood -6352.927929, best rearrangement setting 5 Bootstrap[43]: Time 1.328863 seconds, bootstrap likelihood -6032.603786, best rearrangement setting 14 Bootstrap[44]: Time 1.625047 seconds, bootstrap likelihood -6239.001254, best rearrangement setting 10 Bootstrap[45]: Time 1.460798 seconds, bootstrap likelihood -6079.146201, best rearrangement setting 15 Bootstrap[46]: Time 1.496645 seconds, bootstrap likelihood -6213.750705, best rearrangement setting 14 Bootstrap[47]: Time 1.459651 seconds, bootstrap likelihood -5915.685369, best rearrangement setting 8 Bootstrap[48]: Time 1.639935 seconds, bootstrap likelihood -6306.341657, best rearrangement setting 6 Bootstrap[49]: Time 1.665298 seconds, bootstrap likelihood -6000.787538, best rearrangement setting 7 Bootstrap[50]: Time 0.610769 seconds, bootstrap likelihood -5963.485169, best rearrangement setting 7 Bootstrap[51]: Time 1.657430 seconds, bootstrap likelihood -6163.835989, best rearrangement setting 11 Bootstrap[52]: Time 1.656017 seconds, bootstrap likelihood -5994.810346, best rearrangement setting 12 Bootstrap[53]: Time 1.461915 seconds, bootstrap likelihood -5627.618603, best rearrangement setting 8 Bootstrap[54]: Time 1.531823 seconds, bootstrap likelihood -6226.838484, best rearrangement setting 9 Bootstrap[55]: Time 1.775984 seconds, bootstrap likelihood -5774.545183, best rearrangement setting 11 Bootstrap[56]: Time 1.908450 seconds, bootstrap likelihood -5632.093949, best rearrangement setting 5 Bootstrap[57]: Time 1.588258 seconds, bootstrap likelihood -5899.305016, best rearrangement setting 7 Bootstrap[58]: Time 1.353470 seconds, bootstrap likelihood -6346.471913, best rearrangement setting 10 Bootstrap[59]: Time 1.845530 seconds, bootstrap likelihood -6137.334934, best rearrangement setting 9 Bootstrap[60]: Time 1.538094 seconds, bootstrap likelihood -6471.055114, best rearrangement setting 7 Bootstrap[61]: Time 1.625371 seconds, bootstrap likelihood -6133.078728, best rearrangement setting 5 Bootstrap[62]: Time 1.571677 seconds, bootstrap likelihood -6033.158328, best rearrangement setting 11 Bootstrap[63]: Time 1.360030 seconds, bootstrap likelihood -6150.959141, best rearrangement setting 12 Bootstrap[64]: Time 1.876500 seconds, bootstrap likelihood -6153.028467, best rearrangement setting 7 Bootstrap[65]: Time 1.397877 seconds, bootstrap likelihood -6041.766779, best rearrangement setting 5 Bootstrap[66]: Time 1.714164 seconds, bootstrap likelihood -6181.588705, best rearrangement setting 5 Bootstrap[67]: Time 1.575278 seconds, bootstrap likelihood -6016.386427, best rearrangement setting 15 Bootstrap[68]: Time 1.509965 seconds, bootstrap likelihood -6020.627190, best rearrangement setting 11 Bootstrap[69]: Time 1.822452 seconds, bootstrap likelihood -6072.887278, best rearrangement setting 5 Bootstrap[70]: Time 0.582529 seconds, bootstrap likelihood -5910.416171, best rearrangement setting 8 Bootstrap[71]: Time 1.452488 seconds, bootstrap likelihood -5998.930820, best rearrangement setting 10 Bootstrap[72]: Time 1.458682 seconds, bootstrap likelihood -6142.302098, best rearrangement setting 11 Bootstrap[73]: Time 1.563226 seconds, bootstrap likelihood -6063.426344, best rearrangement setting 9 Bootstrap[74]: Time 1.498088 seconds, bootstrap likelihood -5957.531313, best rearrangement setting 5 Bootstrap[75]: Time 2.211466 seconds, bootstrap likelihood -6228.601564, best rearrangement setting 8 Bootstrap[76]: Time 1.337079 seconds, bootstrap likelihood -5746.640242, best rearrangement setting 9 Bootstrap[77]: Time 1.717788 seconds, bootstrap likelihood -5985.201354, best rearrangement setting 11 Bootstrap[78]: Time 1.608832 seconds, bootstrap likelihood -6135.676827, best rearrangement setting 15 Bootstrap[79]: Time 1.536393 seconds, bootstrap likelihood -6054.959955, best rearrangement setting 9 Bootstrap[80]: Time 1.554436 seconds, bootstrap likelihood -5799.221565, best rearrangement setting 15 Bootstrap[81]: Time 1.738322 seconds, bootstrap likelihood -6173.348295, best rearrangement setting 7 Bootstrap[82]: Time 1.580744 seconds, bootstrap likelihood -6389.748404, best rearrangement setting 6 Bootstrap[83]: Time 1.554058 seconds, bootstrap likelihood -6189.610293, best rearrangement setting 10 Bootstrap[84]: Time 1.739318 seconds, bootstrap likelihood -6333.295517, best rearrangement setting 11 Bootstrap[85]: Time 1.772506 seconds, bootstrap likelihood -6042.871108, best rearrangement setting 8 Bootstrap[86]: Time 1.708615 seconds, bootstrap likelihood -5935.032817, best rearrangement setting 7 Bootstrap[87]: Time 1.463314 seconds, bootstrap likelihood -5855.551980, best rearrangement setting 7 Bootstrap[88]: Time 1.546979 seconds, bootstrap likelihood -5743.726187, best rearrangement setting 12 Bootstrap[89]: Time 1.535511 seconds, bootstrap likelihood -6122.857303, best rearrangement setting 10 Bootstrap[90]: Time 2.071905 seconds, bootstrap likelihood -6017.816466, best rearrangement setting 8 Bootstrap[91]: Time 1.681978 seconds, bootstrap likelihood -6192.927690, best rearrangement setting 12 Bootstrap[92]: Time 1.701920 seconds, bootstrap likelihood -6039.543709, best rearrangement setting 13 Bootstrap[93]: Time 1.596797 seconds, bootstrap likelihood -6040.964678, best rearrangement setting 15 Bootstrap[94]: Time 1.659688 seconds, bootstrap likelihood -5868.131616, best rearrangement setting 5 Bootstrap[95]: Time 1.464431 seconds, bootstrap likelihood -6104.770064, best rearrangement setting 5 Bootstrap[96]: Time 1.551219 seconds, bootstrap likelihood -5703.776336, best rearrangement setting 13 Bootstrap[97]: Time 1.592422 seconds, bootstrap likelihood -6250.245825, best rearrangement setting 11 Bootstrap[98]: Time 1.759395 seconds, bootstrap likelihood -5810.891971, best rearrangement setting 6 Bootstrap[99]: Time 1.737583 seconds, bootstrap likelihood -6328.352144, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 177.070955 seconds Average Time per Rapid Bootstrap 1.770710 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 193.824573 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 16.485706 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.969259 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.058840 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 100.042001 seconds Printed linked AA GTR matrix that achieved an overall improvement of 195.084342 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 16.754992 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.048465 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.070576 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Slow ML Search 0 Likelihood: -6046.424888 Slow ML Search 1 Likelihood: -6046.424888 Slow ML Search 2 Likelihood: -6046.424888 Slow ML Search 3 Likelihood: -6046.424888 Slow ML Search 4 Likelihood: -6046.424888 Slow ML Search 5 Likelihood: -6046.424888 Slow ML Search 6 Likelihood: -6046.424888 Slow ML Search 7 Likelihood: -6046.424890 Slow ML Search 8 Likelihood: -6046.424891 Slow ML Search 9 Likelihood: -6046.424891 Slow ML optimization finished Slow ML search Time: 72.085704 seconds Printed linked AA GTR matrix that achieved an overall improvement of 195.085224 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 16.751753 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.047758 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.070497 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Thorough ML search Time: 32.650255 seconds Final ML Optimization Likelihood: -6046.424964 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.373069 Tree-Length: 7.225935 rate A <-> R: 0.000000 rate A <-> N: 0.000000 rate A <-> D: 0.000000 rate A <-> C: 25.660652 rate A <-> Q: 0.000000 rate A <-> E: 0.000000 rate A <-> G: 42.668962 rate A <-> H: 14.147872 rate A <-> I: 1.256657 rate A <-> L: 1.732609 rate A <-> K: 0.000000 rate A <-> M: 0.079885 rate A <-> F: 0.310067 rate A <-> P: 0.000000 rate A <-> S: 39.980588 rate A <-> T: 15.455539 rate A <-> W: 0.000000 rate A <-> Y: 0.000000 rate A <-> V: 12.558145 rate R <-> N: 0.000000 rate R <-> D: 0.000000 rate R <-> C: 0.000000 rate R <-> Q: 0.000000 rate R <-> E: 0.000000 rate R <-> G: 17.520773 rate R <-> H: 56.168220 rate R <-> I: 0.000000 rate R <-> L: 2.443319 rate R <-> K: 137.947144 rate R <-> M: 0.000000 rate R <-> F: 0.000000 rate R <-> P: 0.000000 rate R <-> S: 4.528066 rate R <-> T: 0.000000 rate R <-> W: 0.000000 rate R <-> Y: 0.000000 rate R <-> V: 0.000000 rate N <-> D: 12.705757 rate N <-> C: 0.523974 rate N <-> Q: 8.592545 rate N <-> E: 5.115475 rate N <-> G: 3.684474 rate N <-> H: 23.919137 rate N <-> I: 1.982970 rate N <-> L: 0.297347 rate N <-> K: 3.355651 rate N <-> M: 6.515843 rate N <-> F: 0.240400 rate N <-> P: 0.000000 rate N <-> S: 9.569200 rate N <-> T: 6.673417 rate N <-> W: 2.417668 rate N <-> Y: 2.121291 rate N <-> V: 0.000000 rate D <-> C: 0.000000 rate D <-> Q: 16.840464 rate D <-> E: 72.072263 rate D <-> G: 20.355210 rate D <-> H: 35.275725 rate D <-> I: 0.000000 rate D <-> L: 0.000000 rate D <-> K: 0.000000 rate D <-> M: 0.000000 rate D <-> F: 0.000000 rate D <-> P: 0.000000 rate D <-> S: 1.853942 rate D <-> T: 0.652014 rate D <-> W: 0.000000 rate D <-> Y: 0.826774 rate D <-> V: 0.000000 rate C <-> Q: 0.000000 rate C <-> E: 0.000000 rate C <-> G: 15.965256 rate C <-> H: 14.920491 rate C <-> I: 1.975112 rate C <-> L: 0.000000 rate C <-> K: 0.000000 rate C <-> M: 0.000000 rate C <-> F: 1.141077 rate C <-> P: 0.000000 rate C <-> S: 12.741879 rate C <-> T: 11.384511 rate C <-> W: 0.000000 rate C <-> Y: 5.867573 rate C <-> V: 0.000000 rate Q <-> E: 9.960995 rate Q <-> G: 0.000000 rate Q <-> H: 54.440963 rate Q <-> I: 2.728701 rate Q <-> L: 0.000000 rate Q <-> K: 17.558404 rate Q <-> M: 12.941385 rate Q <-> F: 0.241175 rate Q <-> P: 0.000000 rate Q <-> S: 0.000000 rate Q <-> T: 7.023287 rate Q <-> W: 0.000000 rate Q <-> Y: 0.319744 rate Q <-> V: 0.000000 rate E <-> G: 4.198979 rate E <-> H: 0.000000 rate E <-> I: 1.051711 rate E <-> L: 0.000000 rate E <-> K: 0.000000 rate E <-> M: 0.000000 rate E <-> F: 0.000000 rate E <-> P: 0.000000 rate E <-> S: 0.000000 rate E <-> T: 2.173044 rate E <-> W: 7.344353 rate E <-> Y: 0.000000 rate E <-> V: 0.000000 rate G <-> H: 0.000000 rate G <-> I: 0.000000 rate G <-> L: 1.159807 rate G <-> K: 0.000000 rate G <-> M: 0.000000 rate G <-> F: 0.317547 rate G <-> P: 0.000000 rate G <-> S: 4.885302 rate G <-> T: 0.000000 rate G <-> W: 0.000000 rate G <-> Y: 0.000000 rate G <-> V: 2.096934 rate H <-> I: 2.602513 rate H <-> L: 3.085123 rate H <-> K: 7.796139 rate H <-> M: 0.000000 rate H <-> F: 1.167810 rate H <-> P: 0.000000 rate H <-> S: 0.000000 rate H <-> T: 0.000000 rate H <-> W: 0.000000 rate H <-> Y: 49.593965 rate H <-> V: 0.000000 rate I <-> L: 16.703024 rate I <-> K: 0.000000 rate I <-> M: 32.795593 rate I <-> F: 1.946919 rate I <-> P: 0.000000 rate I <-> S: 0.000000 rate I <-> T: 12.291513 rate I <-> W: 0.806823 rate I <-> Y: 1.211879 rate I <-> V: 75.182153 rate L <-> K: 0.321557 rate L <-> M: 35.925134 rate L <-> F: 4.587229 rate L <-> P: 0.000000 rate L <-> S: 1.688355 rate L <-> T: 0.916679 rate L <-> W: 0.992544 rate L <-> Y: 1.384128 rate L <-> V: 8.182900 rate K <-> M: 4.299667 rate K <-> F: 0.142874 rate K <-> P: 0.000000 rate K <-> S: 2.032109 rate K <-> T: 1.325681 rate K <-> W: 1.790452 rate K <-> Y: 0.155687 rate K <-> V: 0.403766 rate M <-> F: 3.638278 rate M <-> P: 0.000000 rate M <-> S: 0.000000 rate M <-> T: 12.332759 rate M <-> W: 0.000000 rate M <-> Y: 0.000000 rate M <-> V: 17.848617 rate F <-> P: 0.000000 rate F <-> S: 0.883471 rate F <-> T: 0.000000 rate F <-> W: 0.651404 rate F <-> Y: 6.011933 rate F <-> V: 1.433440 rate P <-> S: 2.431987 rate P <-> T: 5.398000 rate P <-> W: 0.000000 rate P <-> Y: 0.271127 rate P <-> V: 0.000000 rate S <-> T: 14.031316 rate S <-> W: 1.490132 rate S <-> Y: 0.687508 rate S <-> V: 4.330092 rate T <-> W: 0.000000 rate T <-> Y: 2.623794 rate T <-> V: 14.862901 rate W <-> Y: 0.000000 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.027176 freq pi(R): 0.008947 freq pi(N): 0.074086 freq pi(D): 0.013128 freq pi(C): 0.010787 freq pi(Q): 0.012209 freq pi(E): 0.015135 freq pi(G): 0.024082 freq pi(H): 0.004850 freq pi(I): 0.082365 freq pi(L): 0.141734 freq pi(K): 0.047412 freq pi(M): 0.011122 freq pi(F): 0.248766 freq pi(P): 0.012627 freq pi(S): 0.101095 freq pi(T): 0.052262 freq pi(W): 0.010536 freq pi(Y): 0.060958 freq pi(V): 0.040723 ML search took 204.872563 secs or 0.056909 hours Combined Bootstrap and ML search took 381.944317 secs or 0.106096 hours Drawing Bootstrap Support Values on best-scoring ML tree ... Found 1 tree in File /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea Found 1 tree in File /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea Program execution info written to /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bootstrap.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea Best-scoring ML tree written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea Best-scoring ML tree with support values written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitions.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea Best-scoring ML tree with support values as branch labels written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitionsBranchLabels.RAxML-PROTGAMMAGTR-Ymf65.renamed.muscle.Oligohymenophorea Overall execution time for full ML analysis: 381.961470 secs or 0.106100 hours or 0.004421 days