IMPORTANT WARNING: Alignment column 1 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 3 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 8 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 9 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 10 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 11 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 12 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 13 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 15 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 16 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 17 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 18 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 19 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 20 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 21 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 22 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Sequences P_multimicronucleatum-Sample_M04_60aa-ORF_renamed_min100aa_ORF and P_multimicronucleatum-Sample_M05_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: Sequences P_tetraurelia-Sample_291_60aa-ORF_renamed_min100aa_ORF and Paramecium_aurelia are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_127_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_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_131_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_137_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_Indo1-7I_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_Moz13BIII_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_132_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_133_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING Found 11 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. IMPORTANT WARNING Found 22 columns that contain 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 Ymf80.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 80 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 32.38% 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: 80 Name: No Name Provided DataType: AA Substitution Matrix: GTR Using empirical base frequencies RAxML was called as follows: raxml -f a -s Ymf80.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf80.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 49.308505 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.490961 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Time for BS model parameter optimization 7.278325 Bootstrap[0]: Time 8.001012 seconds, bootstrap likelihood -737.707929, best rearrangement setting 13 Bootstrap[1]: Time 0.531477 seconds, bootstrap likelihood -665.627731, best rearrangement setting 13 Bootstrap[2]: Time 0.678214 seconds, bootstrap likelihood -783.646645, best rearrangement setting 12 Bootstrap[3]: Time 0.542670 seconds, bootstrap likelihood -613.488199, best rearrangement setting 15 Bootstrap[4]: Time 0.705384 seconds, bootstrap likelihood -681.659825, best rearrangement setting 10 Bootstrap[5]: Time 0.612482 seconds, bootstrap likelihood -725.301879, best rearrangement setting 10 Bootstrap[6]: Time 0.532586 seconds, bootstrap likelihood -689.407327, best rearrangement setting 6 Bootstrap[7]: Time 0.537233 seconds, bootstrap likelihood -685.395846, best rearrangement setting 14 Bootstrap[8]: Time 0.438817 seconds, bootstrap likelihood -702.824764, best rearrangement setting 5 Bootstrap[9]: Time 0.241414 seconds, bootstrap likelihood -684.430562, best rearrangement setting 7 Bootstrap[10]: Time 0.245082 seconds, bootstrap likelihood -705.811455, best rearrangement setting 7 Bootstrap[11]: Time 0.216821 seconds, bootstrap likelihood -682.547725, best rearrangement setting 5 Bootstrap[12]: Time 0.230601 seconds, bootstrap likelihood -667.954425, best rearrangement setting 8 Bootstrap[13]: Time 0.606085 seconds, bootstrap likelihood -659.019201, best rearrangement setting 7 Bootstrap[14]: Time 0.718834 seconds, bootstrap likelihood -760.744027, best rearrangement setting 12 Bootstrap[15]: Time 0.677252 seconds, bootstrap likelihood -712.693985, best rearrangement setting 15 Bootstrap[16]: Time 0.697361 seconds, bootstrap likelihood -619.638154, best rearrangement setting 12 Bootstrap[17]: Time 0.550371 seconds, bootstrap likelihood -589.574912, best rearrangement setting 12 Bootstrap[18]: Time 0.433548 seconds, bootstrap likelihood -642.502368, best rearrangement setting 5 Bootstrap[19]: Time 0.628429 seconds, bootstrap likelihood -652.493763, best rearrangement setting 8 Bootstrap[20]: Time 0.866168 seconds, bootstrap likelihood -681.229500, best rearrangement setting 10 Bootstrap[21]: Time 0.588605 seconds, bootstrap likelihood -605.737413, best rearrangement setting 6 Bootstrap[22]: Time 0.597694 seconds, bootstrap likelihood -650.918856, best rearrangement setting 5 Bootstrap[23]: Time 0.604570 seconds, bootstrap likelihood -734.093513, best rearrangement setting 7 Bootstrap[24]: Time 0.585191 seconds, bootstrap likelihood -595.469296, best rearrangement setting 8 Bootstrap[25]: Time 0.617796 seconds, bootstrap likelihood -725.893721, best rearrangement setting 6 Bootstrap[26]: Time 0.672228 seconds, bootstrap likelihood -586.201741, best rearrangement setting 12 Bootstrap[27]: Time 0.514445 seconds, bootstrap likelihood -627.232802, best rearrangement setting 10 Bootstrap[28]: Time 0.587211 seconds, bootstrap likelihood -663.762723, best rearrangement setting 11 Bootstrap[29]: Time 0.672438 seconds, bootstrap likelihood -701.153142, best rearrangement setting 12 Bootstrap[30]: Time 0.573841 seconds, bootstrap likelihood -675.069787, best rearrangement setting 15 Bootstrap[31]: Time 0.545792 seconds, bootstrap likelihood -666.359467, best rearrangement setting 15 Bootstrap[32]: Time 0.230325 seconds, bootstrap likelihood -663.726120, best rearrangement setting 6 Bootstrap[33]: Time 0.665067 seconds, bootstrap likelihood -647.526563, best rearrangement setting 15 Bootstrap[34]: Time 0.671873 seconds, bootstrap likelihood -730.576208, best rearrangement setting 11 Bootstrap[35]: Time 0.528201 seconds, bootstrap likelihood -733.040779, best rearrangement setting 8 Bootstrap[36]: Time 0.638676 seconds, bootstrap likelihood -707.523944, best rearrangement setting 9 Bootstrap[37]: Time 0.710605 seconds, bootstrap likelihood -621.250483, best rearrangement setting 11 Bootstrap[38]: Time 0.621305 seconds, bootstrap likelihood -750.704600, best rearrangement setting 8 Bootstrap[39]: Time 0.613488 seconds, bootstrap likelihood -607.170684, best rearrangement setting 13 Bootstrap[40]: Time 0.497814 seconds, bootstrap likelihood -614.982486, best rearrangement setting 13 Bootstrap[41]: Time 0.676669 seconds, bootstrap likelihood -689.424678, best rearrangement setting 10 Bootstrap[42]: Time 0.201740 seconds, bootstrap likelihood -596.376387, best rearrangement setting 5 Bootstrap[43]: Time 0.553978 seconds, bootstrap likelihood -755.092495, best rearrangement setting 14 Bootstrap[44]: Time 0.245692 seconds, bootstrap likelihood -695.133663, best rearrangement setting 10 Bootstrap[45]: Time 0.270803 seconds, bootstrap likelihood -683.008326, best rearrangement setting 15 Bootstrap[46]: Time 0.239645 seconds, bootstrap likelihood -673.525432, best rearrangement setting 14 Bootstrap[47]: Time 0.267237 seconds, bootstrap likelihood -623.355590, best rearrangement setting 8 Bootstrap[48]: Time 0.677425 seconds, bootstrap likelihood -680.777566, best rearrangement setting 6 Bootstrap[49]: Time 0.270841 seconds, bootstrap likelihood -688.413591, best rearrangement setting 7 Bootstrap[50]: Time 0.253913 seconds, bootstrap likelihood -618.563403, best rearrangement setting 7 Bootstrap[51]: Time 0.677522 seconds, bootstrap likelihood -708.645228, best rearrangement setting 11 Bootstrap[52]: Time 0.613655 seconds, bootstrap likelihood -688.056710, best rearrangement setting 12 Bootstrap[53]: Time 0.786568 seconds, bootstrap likelihood -688.679078, best rearrangement setting 8 Bootstrap[54]: Time 0.710187 seconds, bootstrap likelihood -822.885397, best rearrangement setting 9 Bootstrap[55]: Time 0.501774 seconds, bootstrap likelihood -751.082663, best rearrangement setting 11 Bootstrap[56]: Time 0.601289 seconds, bootstrap likelihood -649.843678, best rearrangement setting 5 Bootstrap[57]: Time 0.669202 seconds, bootstrap likelihood -833.046975, best rearrangement setting 7 Bootstrap[58]: Time 0.533367 seconds, bootstrap likelihood -618.353856, best rearrangement setting 10 Bootstrap[59]: Time 0.734778 seconds, bootstrap likelihood -626.885218, best rearrangement setting 9 Bootstrap[60]: Time 0.607724 seconds, bootstrap likelihood -682.005721, best rearrangement setting 7 Bootstrap[61]: Time 0.468981 seconds, bootstrap likelihood -685.569121, best rearrangement setting 5 Bootstrap[62]: Time 0.573243 seconds, bootstrap likelihood -794.555130, best rearrangement setting 11 Bootstrap[63]: Time 0.290793 seconds, bootstrap likelihood -646.080285, best rearrangement setting 12 Bootstrap[64]: Time 0.261674 seconds, bootstrap likelihood -718.516598, best rearrangement setting 7 Bootstrap[65]: Time 0.197499 seconds, bootstrap likelihood -647.948099, best rearrangement setting 5 Bootstrap[66]: Time 0.233838 seconds, bootstrap likelihood -695.922661, best rearrangement setting 5 Bootstrap[67]: Time 0.278881 seconds, bootstrap likelihood -699.195394, best rearrangement setting 15 Bootstrap[68]: Time 0.314752 seconds, bootstrap likelihood -673.425442, best rearrangement setting 11 Bootstrap[69]: Time 0.475895 seconds, bootstrap likelihood -603.789883, best rearrangement setting 5 Bootstrap[70]: Time 0.240411 seconds, bootstrap likelihood -668.438295, best rearrangement setting 8 Bootstrap[71]: Time 0.220452 seconds, bootstrap likelihood -590.044373, best rearrangement setting 10 Bootstrap[72]: Time 0.225464 seconds, bootstrap likelihood -610.466725, best rearrangement setting 11 Bootstrap[73]: Time 0.267910 seconds, bootstrap likelihood -615.006057, best rearrangement setting 9 Bootstrap[74]: Time 0.202370 seconds, bootstrap likelihood -516.832633, best rearrangement setting 5 Bootstrap[75]: Time 0.249591 seconds, bootstrap likelihood -602.837056, best rearrangement setting 8 Bootstrap[76]: Time 0.638738 seconds, bootstrap likelihood -689.294750, best rearrangement setting 9 Bootstrap[77]: Time 0.266570 seconds, bootstrap likelihood -656.447824, best rearrangement setting 11 Bootstrap[78]: Time 0.572219 seconds, bootstrap likelihood -641.509771, best rearrangement setting 15 Bootstrap[79]: Time 0.745581 seconds, bootstrap likelihood -592.677418, best rearrangement setting 9 Bootstrap[80]: Time 0.583231 seconds, bootstrap likelihood -649.091289, best rearrangement setting 15 Bootstrap[81]: Time 0.231909 seconds, bootstrap likelihood -676.995875, best rearrangement setting 7 Bootstrap[82]: Time 0.305222 seconds, bootstrap likelihood -510.192005, best rearrangement setting 6 Bootstrap[83]: Time 0.271734 seconds, bootstrap likelihood -530.546735, best rearrangement setting 10 Bootstrap[84]: Time 0.273067 seconds, bootstrap likelihood -679.317755, best rearrangement setting 11 Bootstrap[85]: Time 0.621769 seconds, bootstrap likelihood -595.344590, best rearrangement setting 8 Bootstrap[86]: Time 0.666290 seconds, bootstrap likelihood -659.634391, best rearrangement setting 7 Bootstrap[87]: Time 0.482133 seconds, bootstrap likelihood -528.094850, best rearrangement setting 7 Bootstrap[88]: Time 0.270592 seconds, bootstrap likelihood -739.097364, best rearrangement setting 12 Bootstrap[89]: Time 0.734077 seconds, bootstrap likelihood -665.465869, best rearrangement setting 10 Bootstrap[90]: Time 0.640031 seconds, bootstrap likelihood -632.254569, best rearrangement setting 8 Bootstrap[91]: Time 0.567534 seconds, bootstrap likelihood -749.676303, best rearrangement setting 12 Bootstrap[92]: Time 0.277192 seconds, bootstrap likelihood -565.651997, best rearrangement setting 13 Bootstrap[93]: Time 0.709712 seconds, bootstrap likelihood -683.148607, best rearrangement setting 15 Bootstrap[94]: Time 0.558224 seconds, bootstrap likelihood -632.387218, best rearrangement setting 5 Bootstrap[95]: Time 0.472075 seconds, bootstrap likelihood -666.903593, best rearrangement setting 5 Bootstrap[96]: Time 0.542015 seconds, bootstrap likelihood -776.188027, best rearrangement setting 13 Bootstrap[97]: Time 0.240059 seconds, bootstrap likelihood -671.627324, best rearrangement setting 11 Bootstrap[98]: Time 0.491432 seconds, bootstrap likelihood -671.406764, best rearrangement setting 6 Bootstrap[99]: Time 0.661166 seconds, bootstrap likelihood -679.737898, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 56.954007 seconds Average Time per Rapid Bootstrap 0.569540 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 51.492999 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.159886 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.742923 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.342645 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.027642 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 43.640453 seconds Printed linked AA GTR matrix that achieved an overall improvement of 52.210232 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.622641 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.365473 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.063403 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Slow ML Search 0 Likelihood: -676.724297 Slow ML Search 1 Likelihood: -676.724297 Slow ML Search 2 Likelihood: -676.724297 Slow ML Search 3 Likelihood: -676.724297 Slow ML Search 4 Likelihood: -676.724297 Slow ML Search 5 Likelihood: -676.724297 Slow ML Search 6 Likelihood: -676.724297 Slow ML Search 7 Likelihood: -676.724297 Slow ML Search 8 Likelihood: -676.724297 Slow ML Search 9 Likelihood: -676.724297 Slow ML optimization finished Slow ML search Time: 24.816173 seconds Printed linked AA GTR matrix that achieved an overall improvement of 52.129982 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.703599 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.367766 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.060930 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-Ymf80.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Thorough ML search Time: 14.444166 seconds Final ML Optimization Likelihood: -676.725579 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 2.384269 Tree-Length: 1.405078 rate A <-> R: 0.000000 rate A <-> N: 0.000000 rate A <-> D: 0.000000 rate A <-> C: 0.000000 rate A <-> Q: 0.000000 rate A <-> E: 0.000000 rate A <-> G: 0.000000 rate A <-> H: 0.000000 rate A <-> I: 0.000000 rate A <-> L: 0.000000 rate A <-> K: 0.000000 rate A <-> M: 0.000000 rate A <-> F: 0.000000 rate A <-> P: 0.000000 rate A <-> S: 17.254060 rate A <-> T: 29.249857 rate A <-> W: 0.000000 rate A <-> Y: 0.000017 rate A <-> V: 0.000000 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: 0.000000 rate R <-> H: 0.000017 rate R <-> I: 9.798417 rate R <-> L: 9.266820 rate R <-> K: 149.469945 rate R <-> M: 0.000000 rate R <-> F: 0.000000 rate R <-> P: 0.000796 rate R <-> S: 0.000000 rate R <-> T: 0.000000 rate R <-> W: 0.000000 rate R <-> Y: 0.000000 rate R <-> V: 0.000017 rate N <-> D: 8.533589 rate N <-> C: 0.000000 rate N <-> Q: 0.000000 rate N <-> E: 0.000000 rate N <-> G: 0.625684 rate N <-> H: 0.000045 rate N <-> I: 0.000000 rate N <-> L: 0.000000 rate N <-> K: 2.510289 rate N <-> M: 0.000000 rate N <-> F: 0.000000 rate N <-> P: 0.000000 rate N <-> S: 7.982626 rate N <-> T: 1.645521 rate N <-> W: 0.000000 rate N <-> Y: 0.000000 rate N <-> V: 0.000000 rate D <-> C: 0.000017 rate D <-> Q: 0.000000 rate D <-> E: 0.000000 rate D <-> G: 0.000000 rate D <-> H: 0.000328 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: 0.000000 rate D <-> T: 0.000000 rate D <-> W: 0.000000 rate D <-> Y: 0.000000 rate D <-> V: 0.000000 rate C <-> Q: 0.000000 rate C <-> E: 0.000000 rate C <-> G: 0.000000 rate C <-> H: 2853.768504 rate C <-> I: 0.000017 rate C <-> L: 40.723840 rate C <-> K: 0.000000 rate C <-> M: 0.000073 rate C <-> F: 39.915424 rate C <-> P: 0.000000 rate C <-> S: 0.000000 rate C <-> T: 0.000000 rate C <-> W: 0.000000 rate C <-> Y: 0.000000 rate C <-> V: 183.636289 rate Q <-> E: 0.000000 rate Q <-> G: 0.000017 rate Q <-> H: 0.000055 rate Q <-> I: 0.000000 rate Q <-> L: 0.000000 rate Q <-> K: 0.000000 rate Q <-> M: 0.000000 rate Q <-> F: 0.000000 rate Q <-> P: 0.000000 rate Q <-> S: 0.000000 rate Q <-> T: 0.000000 rate Q <-> W: 0.000017 rate Q <-> Y: 0.000000 rate Q <-> V: 0.000000 rate E <-> G: 0.000000 rate E <-> H: 0.000000 rate E <-> I: 0.000000 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: 0.000000 rate E <-> W: 0.000000 rate E <-> Y: 0.000000 rate E <-> V: 0.000000 rate G <-> H: 0.000320 rate G <-> I: 0.000000 rate G <-> L: 0.000000 rate G <-> K: 0.000000 rate G <-> M: 0.000000 rate G <-> F: 0.000000 rate G <-> P: 0.000017 rate G <-> S: 11.687061 rate G <-> T: 0.000000 rate G <-> W: 0.000010 rate G <-> Y: 0.000000 rate G <-> V: 0.000000 rate H <-> I: 0.000056 rate H <-> L: 0.001461 rate H <-> K: 0.000055 rate H <-> M: 0.000000 rate H <-> F: 0.000063 rate H <-> P: 0.002713 rate H <-> S: 0.000000 rate H <-> T: 0.000000 rate H <-> W: 0.000120 rate H <-> Y: 0.000010 rate H <-> V: 0.000328 rate I <-> L: 4.575952 rate I <-> K: 2.456568 rate I <-> M: 8.409731 rate I <-> F: 5.524369 rate I <-> P: 0.000000 rate I <-> S: 3.086897 rate I <-> T: 0.898493 rate I <-> W: 0.000000 rate I <-> Y: 0.000000 rate I <-> V: 94.729106 rate L <-> K: 0.000000 rate L <-> M: 5.906854 rate L <-> F: 2.147058 rate L <-> P: 0.000000 rate L <-> S: 1.395691 rate L <-> T: 6.150149 rate L <-> W: 0.000000 rate L <-> Y: 0.000000 rate L <-> V: 0.000000 rate K <-> M: 0.000000 rate K <-> F: 0.000000 rate K <-> P: 0.000017 rate K <-> S: 0.000000 rate K <-> T: 3.180866 rate K <-> W: 0.000000 rate K <-> Y: 0.000000 rate K <-> V: 0.000000 rate M <-> F: 0.000000 rate M <-> P: 0.000000 rate M <-> S: 0.000000 rate M <-> T: 18.500691 rate M <-> W: 0.000017 rate M <-> Y: 0.000017 rate M <-> V: 0.000000 rate F <-> P: 0.000000 rate F <-> S: 0.980679 rate F <-> T: 0.000000 rate F <-> W: 0.000000 rate F <-> Y: 5.261878 rate F <-> V: 0.000000 rate P <-> S: 0.000000 rate P <-> T: 0.000010 rate P <-> W: 0.000000 rate P <-> Y: 0.000316 rate P <-> V: 0.000015 rate S <-> T: 14.981107 rate S <-> W: 0.000000 rate S <-> Y: 0.000000 rate S <-> V: 0.000000 rate T <-> W: 0.000000 rate T <-> Y: 0.000000 rate T <-> V: 37.054519 rate W <-> Y: 0.000000 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.023302 freq pi(R): 0.008477 freq pi(N): 0.127496 freq pi(D): 0.013136 freq pi(C): 0.002124 freq pi(Q): 0.022031 freq pi(E): 0.022454 freq pi(G): 0.013136 freq pi(H): 0.001000 freq pi(I): 0.091494 freq pi(L): 0.166040 freq pi(K): 0.063539 freq pi(M): 0.013983 freq pi(F): 0.212207 freq pi(P): 0.001000 freq pi(S): 0.087682 freq pi(T): 0.052103 freq pi(W): 0.011018 freq pi(Y): 0.013136 freq pi(V): 0.054645 ML search took 82.994904 secs or 0.023054 hours Combined Bootstrap and ML search took 139.949761 secs or 0.038875 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-Ymf80.renamed.muscle.Oligohymenophorea Found 1 tree in File /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-Ymf80.renamed.muscle.Oligohymenophorea Program execution info written to /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-Ymf80.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-Ymf80.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-Ymf80.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-Ymf80.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-Ymf80.renamed.muscle.Oligohymenophorea Overall execution time for full ML analysis: 139.963922 secs or 0.038879 hours or 0.001620 days