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_biaurelia-Sample_379_60aa-ORF_renamed_min100aa_ORF and P_biaurelia-Sample_USBL-36I1_60aa-ORF_renamed_min100aa_ORF 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_130_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_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_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: 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 Found 13 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 Ymf78.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 82 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 40.39% 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: 82 Name: No Name Provided DataType: AA Substitution Matrix: GTR Using empirical base frequencies RAxML was called as follows: raxml -f a -s Ymf78.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-Ymf78.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 57.223239 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 9.283029 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.015372 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Time for BS model parameter optimization 10.593075 Bootstrap[0]: Time 10.917885 seconds, bootstrap likelihood -986.714814, best rearrangement setting 13 Bootstrap[1]: Time 0.220988 seconds, bootstrap likelihood -740.637681, best rearrangement setting 13 Bootstrap[2]: Time 0.525726 seconds, bootstrap likelihood -839.079145, best rearrangement setting 12 Bootstrap[3]: Time 0.591935 seconds, bootstrap likelihood -865.058270, best rearrangement setting 15 Bootstrap[4]: Time 0.255554 seconds, bootstrap likelihood -876.046160, best rearrangement setting 10 Bootstrap[5]: Time 0.721630 seconds, bootstrap likelihood -894.502434, best rearrangement setting 10 Bootstrap[6]: Time 0.538235 seconds, bootstrap likelihood -833.238905, best rearrangement setting 6 Bootstrap[7]: Time 0.647641 seconds, bootstrap likelihood -895.070310, best rearrangement setting 14 Bootstrap[8]: Time 0.230956 seconds, bootstrap likelihood -861.642373, best rearrangement setting 5 Bootstrap[9]: Time 0.214866 seconds, bootstrap likelihood -941.653143, best rearrangement setting 7 Bootstrap[10]: Time 0.266234 seconds, bootstrap likelihood -886.673621, best rearrangement setting 7 Bootstrap[11]: Time 0.227188 seconds, bootstrap likelihood -864.915497, best rearrangement setting 5 Bootstrap[12]: Time 0.237062 seconds, bootstrap likelihood -827.119885, best rearrangement setting 8 Bootstrap[13]: Time 0.712972 seconds, bootstrap likelihood -817.864756, best rearrangement setting 7 Bootstrap[14]: Time 0.786712 seconds, bootstrap likelihood -875.116768, best rearrangement setting 12 Bootstrap[15]: Time 0.604531 seconds, bootstrap likelihood -798.579994, best rearrangement setting 15 Bootstrap[16]: Time 0.543861 seconds, bootstrap likelihood -881.363873, best rearrangement setting 12 Bootstrap[17]: Time 0.246709 seconds, bootstrap likelihood -805.352468, best rearrangement setting 12 Bootstrap[18]: Time 0.496916 seconds, bootstrap likelihood -772.319615, best rearrangement setting 5 Bootstrap[19]: Time 0.229674 seconds, bootstrap likelihood -924.579384, best rearrangement setting 8 Bootstrap[20]: Time 0.231205 seconds, bootstrap likelihood -859.234337, best rearrangement setting 10 Bootstrap[21]: Time 0.222028 seconds, bootstrap likelihood -932.853836, best rearrangement setting 6 Bootstrap[22]: Time 0.227817 seconds, bootstrap likelihood -851.022125, best rearrangement setting 5 Bootstrap[23]: Time 0.273248 seconds, bootstrap likelihood -769.266619, best rearrangement setting 7 Bootstrap[24]: Time 0.234491 seconds, bootstrap likelihood -837.106440, best rearrangement setting 8 Bootstrap[25]: Time 0.246048 seconds, bootstrap likelihood -810.537353, best rearrangement setting 6 Bootstrap[26]: Time 0.579337 seconds, bootstrap likelihood -755.826384, best rearrangement setting 12 Bootstrap[27]: Time 0.570962 seconds, bootstrap likelihood -853.479967, best rearrangement setting 10 Bootstrap[28]: Time 0.345995 seconds, bootstrap likelihood -802.345220, best rearrangement setting 11 Bootstrap[29]: Time 0.625504 seconds, bootstrap likelihood -886.692351, best rearrangement setting 12 Bootstrap[30]: Time 0.634159 seconds, bootstrap likelihood -775.092196, best rearrangement setting 15 Bootstrap[31]: Time 0.564151 seconds, bootstrap likelihood -820.864326, best rearrangement setting 15 Bootstrap[32]: Time 0.224408 seconds, bootstrap likelihood -915.924636, best rearrangement setting 6 Bootstrap[33]: Time 0.583359 seconds, bootstrap likelihood -998.318732, best rearrangement setting 15 Bootstrap[34]: Time 0.604348 seconds, bootstrap likelihood -808.894267, best rearrangement setting 11 Bootstrap[35]: Time 0.673376 seconds, bootstrap likelihood -848.296375, best rearrangement setting 8 Bootstrap[36]: Time 0.646585 seconds, bootstrap likelihood -862.735810, best rearrangement setting 9 Bootstrap[37]: Time 0.779445 seconds, bootstrap likelihood -838.233056, best rearrangement setting 11 Bootstrap[38]: Time 0.560080 seconds, bootstrap likelihood -830.981537, best rearrangement setting 8 Bootstrap[39]: Time 0.647491 seconds, bootstrap likelihood -874.679842, best rearrangement setting 13 Bootstrap[40]: Time 0.243861 seconds, bootstrap likelihood -825.454736, best rearrangement setting 13 Bootstrap[41]: Time 0.561496 seconds, bootstrap likelihood -826.876055, best rearrangement setting 10 Bootstrap[42]: Time 0.541835 seconds, bootstrap likelihood -868.015022, best rearrangement setting 5 Bootstrap[43]: Time 0.227792 seconds, bootstrap likelihood -861.345389, best rearrangement setting 14 Bootstrap[44]: Time 0.232951 seconds, bootstrap likelihood -827.101412, best rearrangement setting 10 Bootstrap[45]: Time 0.232510 seconds, bootstrap likelihood -783.976932, best rearrangement setting 15 Bootstrap[46]: Time 0.240764 seconds, bootstrap likelihood -764.402234, best rearrangement setting 14 Bootstrap[47]: Time 0.266958 seconds, bootstrap likelihood -869.742715, best rearrangement setting 8 Bootstrap[48]: Time 0.245231 seconds, bootstrap likelihood -889.894933, best rearrangement setting 6 Bootstrap[49]: Time 0.244950 seconds, bootstrap likelihood -858.155688, best rearrangement setting 7 Bootstrap[50]: Time 0.565125 seconds, bootstrap likelihood -936.059229, best rearrangement setting 7 Bootstrap[51]: Time 0.219826 seconds, bootstrap likelihood -868.757970, best rearrangement setting 11 Bootstrap[52]: Time 0.341250 seconds, bootstrap likelihood -845.664072, best rearrangement setting 12 Bootstrap[53]: Time 0.477502 seconds, bootstrap likelihood -766.312443, best rearrangement setting 8 Bootstrap[54]: Time 0.252544 seconds, bootstrap likelihood -812.831827, best rearrangement setting 9 Bootstrap[55]: Time 0.397932 seconds, bootstrap likelihood -773.120026, best rearrangement setting 11 Bootstrap[56]: Time 0.273393 seconds, bootstrap likelihood -846.061338, best rearrangement setting 5 Bootstrap[57]: Time 0.768946 seconds, bootstrap likelihood -829.574066, best rearrangement setting 7 Bootstrap[58]: Time 0.236772 seconds, bootstrap likelihood -797.488993, best rearrangement setting 10 Bootstrap[59]: Time 0.230193 seconds, bootstrap likelihood -915.480824, best rearrangement setting 9 Bootstrap[60]: Time 0.613731 seconds, bootstrap likelihood -833.385428, best rearrangement setting 7 Bootstrap[61]: Time 0.602674 seconds, bootstrap likelihood -841.089686, best rearrangement setting 5 Bootstrap[62]: Time 0.680900 seconds, bootstrap likelihood -818.633542, best rearrangement setting 11 Bootstrap[63]: Time 0.263821 seconds, bootstrap likelihood -806.294247, best rearrangement setting 12 Bootstrap[64]: Time 0.708658 seconds, bootstrap likelihood -870.585619, best rearrangement setting 7 Bootstrap[65]: Time 0.748559 seconds, bootstrap likelihood -869.271855, best rearrangement setting 5 Bootstrap[66]: Time 0.554978 seconds, bootstrap likelihood -903.392222, best rearrangement setting 5 Bootstrap[67]: Time 0.700314 seconds, bootstrap likelihood -778.909280, best rearrangement setting 15 Bootstrap[68]: Time 0.285202 seconds, bootstrap likelihood -859.384626, best rearrangement setting 11 Bootstrap[69]: Time 0.233853 seconds, bootstrap likelihood -842.070796, best rearrangement setting 5 Bootstrap[70]: Time 0.662240 seconds, bootstrap likelihood -826.702743, best rearrangement setting 8 Bootstrap[71]: Time 0.546788 seconds, bootstrap likelihood -760.656768, best rearrangement setting 10 Bootstrap[72]: Time 0.584571 seconds, bootstrap likelihood -832.987880, best rearrangement setting 11 Bootstrap[73]: Time 0.250012 seconds, bootstrap likelihood -884.015201, best rearrangement setting 9 Bootstrap[74]: Time 0.304280 seconds, bootstrap likelihood -872.346526, best rearrangement setting 5 Bootstrap[75]: Time 0.244057 seconds, bootstrap likelihood -806.599949, best rearrangement setting 8 Bootstrap[76]: Time 0.497336 seconds, bootstrap likelihood -768.039998, best rearrangement setting 9 Bootstrap[77]: Time 0.700782 seconds, bootstrap likelihood -830.112873, best rearrangement setting 11 Bootstrap[78]: Time 0.699292 seconds, bootstrap likelihood -869.268898, best rearrangement setting 15 Bootstrap[79]: Time 0.301570 seconds, bootstrap likelihood -830.300056, best rearrangement setting 9 Bootstrap[80]: Time 0.268881 seconds, bootstrap likelihood -744.255804, best rearrangement setting 15 Bootstrap[81]: Time 0.253384 seconds, bootstrap likelihood -874.615646, best rearrangement setting 7 Bootstrap[82]: Time 0.510733 seconds, bootstrap likelihood -968.303185, best rearrangement setting 6 Bootstrap[83]: Time 0.585484 seconds, bootstrap likelihood -777.546785, best rearrangement setting 10 Bootstrap[84]: Time 0.396228 seconds, bootstrap likelihood -812.898159, best rearrangement setting 11 Bootstrap[85]: Time 0.348400 seconds, bootstrap likelihood -834.778435, best rearrangement setting 8 Bootstrap[86]: Time 0.540840 seconds, bootstrap likelihood -795.629025, best rearrangement setting 7 Bootstrap[87]: Time 0.992150 seconds, bootstrap likelihood -873.968261, best rearrangement setting 7 Bootstrap[88]: Time 0.229488 seconds, bootstrap likelihood -771.846887, best rearrangement setting 12 Bootstrap[89]: Time 0.581313 seconds, bootstrap likelihood -787.670239, best rearrangement setting 10 Bootstrap[90]: Time 0.262950 seconds, bootstrap likelihood -840.313787, best rearrangement setting 8 Bootstrap[91]: Time 0.232063 seconds, bootstrap likelihood -840.063444, best rearrangement setting 12 Bootstrap[92]: Time 0.276314 seconds, bootstrap likelihood -908.184886, best rearrangement setting 13 Bootstrap[93]: Time 0.237973 seconds, bootstrap likelihood -795.354852, best rearrangement setting 15 Bootstrap[94]: Time 0.577051 seconds, bootstrap likelihood -773.964792, best rearrangement setting 5 Bootstrap[95]: Time 0.742536 seconds, bootstrap likelihood -880.968083, best rearrangement setting 5 Bootstrap[96]: Time 0.542291 seconds, bootstrap likelihood -825.724678, best rearrangement setting 13 Bootstrap[97]: Time 0.621958 seconds, bootstrap likelihood -867.226071, best rearrangement setting 11 Bootstrap[98]: Time 0.285251 seconds, bootstrap likelihood -861.900064, best rearrangement setting 6 Bootstrap[99]: Time 0.296847 seconds, bootstrap likelihood -890.608260, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 54.563799 seconds Average Time per Rapid Bootstrap 0.545638 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 57.223464 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 9.282874 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.015336 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.651045 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.131207 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.039577 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 38.867911 seconds Printed linked AA GTR matrix that achieved an overall improvement of 57.223430 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 9.283148 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.015146 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.650978 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.131212 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.039590 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Slow ML Search 0 Likelihood: -850.310922 Slow ML Search 1 Likelihood: -850.310922 Slow ML Search 2 Likelihood: -850.310922 Slow ML Search 3 Likelihood: -850.310922 Slow ML Search 4 Likelihood: -850.310922 Slow ML Search 5 Likelihood: -850.310922 Slow ML Search 6 Likelihood: -850.310922 Slow ML Search 7 Likelihood: -850.310922 Slow ML Search 8 Likelihood: -850.310922 Slow ML Search 9 Likelihood: -850.310922 Slow ML optimization finished Slow ML search Time: 30.812357 seconds Printed linked AA GTR matrix that achieved an overall improvement of 57.223430 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 9.283147 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.015146 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.650978 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.131212 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.039590 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-Ymf78.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Thorough ML search Time: 20.410576 seconds Final ML Optimization Likelihood: -850.310922 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 5.303522 Tree-Length: 2.730867 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: 3.035021 rate A <-> M: 0.000000 rate A <-> F: 8.279503 rate A <-> P: 0.000000 rate A <-> S: 67.843038 rate A <-> T: 76.381947 rate A <-> W: 0.000000 rate A <-> Y: 0.000000 rate A <-> V: 0.000000 rate R <-> N: 7.083345 rate R <-> D: 0.000000 rate R <-> C: 0.000000 rate R <-> Q: 11.584847 rate R <-> E: 0.000000 rate R <-> G: 0.000000 rate R <-> H: 6.380781 rate R <-> I: 0.000000 rate R <-> L: 0.000000 rate R <-> K: 16.668925 rate R <-> M: 7.434755 rate R <-> F: 0.000000 rate R <-> P: 0.000000 rate R <-> S: 0.000000 rate R <-> T: 0.000000 rate R <-> W: 6.942072 rate R <-> Y: 0.000000 rate R <-> V: 0.000000 rate N <-> D: 3.139779 rate N <-> C: 0.000000 rate N <-> Q: 0.000000 rate N <-> E: 0.000000 rate N <-> G: 5.508826 rate N <-> H: 0.000000 rate N <-> I: 0.000000 rate N <-> L: 2.192246 rate N <-> K: 5.854136 rate N <-> M: 0.000000 rate N <-> F: 0.000000 rate N <-> P: 0.000000 rate N <-> S: 9.436301 rate N <-> T: 30.001087 rate N <-> W: 0.000000 rate N <-> Y: 0.000000 rate N <-> V: 0.000000 rate D <-> C: 0.000000 rate D <-> Q: 0.000000 rate D <-> E: 0.000000 rate D <-> G: 0.000000 rate D <-> H: 0.000000 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: 7.510611 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: 12.538056 rate C <-> H: 0.000000 rate C <-> I: 0.000000 rate C <-> L: 0.000000 rate C <-> K: 0.000000 rate C <-> M: 9.418608 rate C <-> F: 0.974331 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: 0.000000 rate Q <-> E: 0.000000 rate Q <-> G: 0.000000 rate Q <-> H: 0.000000 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: 236.237824 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: 12.018470 rate E <-> T: 0.000000 rate E <-> W: 0.000000 rate E <-> Y: 0.000000 rate E <-> V: 0.000000 rate G <-> H: 0.000000 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: 0.000000 rate G <-> S: 20.425896 rate G <-> T: 0.000000 rate G <-> W: 0.000000 rate G <-> Y: 0.000000 rate G <-> V: 0.000000 rate H <-> I: 0.000000 rate H <-> L: 0.000000 rate H <-> K: 0.000000 rate H <-> M: 0.000000 rate H <-> F: 0.000000 rate H <-> P: 0.000000 rate H <-> S: 0.000000 rate H <-> T: 0.000000 rate H <-> W: 0.000000 rate H <-> Y: 5.714768 rate H <-> V: 0.000000 rate I <-> L: 0.000000 rate I <-> K: 0.000000 rate I <-> M: 0.000000 rate I <-> F: 0.000000 rate I <-> P: 19.228300 rate I <-> S: 0.000000 rate I <-> T: 20.519010 rate I <-> W: 0.000000 rate I <-> Y: 0.000000 rate I <-> V: 124.564507 rate L <-> K: 0.000000 rate L <-> M: 10.963803 rate L <-> F: 4.730651 rate L <-> P: 0.000000 rate L <-> S: 0.000000 rate L <-> T: 0.000000 rate L <-> W: 14.148734 rate L <-> Y: 2.489757 rate L <-> V: 22.520776 rate K <-> M: 0.000000 rate K <-> F: 0.000000 rate K <-> P: 0.000000 rate K <-> S: 0.000000 rate K <-> T: 0.000000 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: 14.126169 rate M <-> T: 21.161722 rate M <-> W: 0.000000 rate M <-> Y: 0.000000 rate M <-> V: 24.250801 rate F <-> P: 0.000000 rate F <-> S: 3.652311 rate F <-> T: 0.117650 rate F <-> W: 0.000000 rate F <-> Y: 5.085649 rate F <-> V: 0.366749 rate P <-> S: 0.000000 rate P <-> T: 0.000000 rate P <-> W: 0.000000 rate P <-> Y: 0.000000 rate P <-> V: 0.000000 rate S <-> T: 3.876822 rate S <-> W: 34.769053 rate S <-> Y: 0.000000 rate S <-> V: 0.000000 rate T <-> W: 0.000000 rate T <-> Y: 0.000000 rate T <-> V: 48.404493 rate W <-> Y: 0.000000 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.022882 freq pi(R): 0.081489 freq pi(N): 0.056159 freq pi(D): 0.032815 freq pi(C): 0.042252 freq pi(Q): 0.009969 freq pi(E): 0.014935 freq pi(G): 0.027352 freq pi(H): 0.020895 freq pi(I): 0.049205 freq pi(L): 0.107315 freq pi(K): 0.085959 freq pi(M): 0.021392 freq pi(F): 0.202675 freq pi(P): 0.011955 freq pi(S): 0.039272 freq pi(T): 0.041259 freq pi(W): 0.006989 freq pi(Y): 0.083972 freq pi(V): 0.041259 ML search took 90.192258 secs or 0.025053 hours Combined Bootstrap and ML search took 144.756901 secs or 0.040210 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-Ymf78.renamed.muscle.Oligohymenophorea Found 1 tree in File /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-Ymf78.renamed.muscle.Oligohymenophorea Program execution info written to /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-Ymf78.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-Ymf78.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-Ymf78.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-Ymf78.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-Ymf78.renamed.muscle.Oligohymenophorea Overall execution time for full ML analysis: 144.772174 secs or 0.040214 hours or 0.001676 days