IMPORTANT WARNING: Alignment column 383 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 384 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 595 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 596 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 597 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 598 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 599 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 600 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 601 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 602 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 603 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 604 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 605 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 606 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 607 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 608 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 628 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 629 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 630 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 631 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 632 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 633 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 634 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 635 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 636 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 637 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 660 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 661 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 662 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 663 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 664 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 665 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 666 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 667 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 668 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 669 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 670 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 671 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 672 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 673 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 674 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 675 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 691 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 692 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 693 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 702 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 703 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 733 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 734 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 735 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 736 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 768 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 812 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 813 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 814 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 815 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 816 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 817 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 818 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 819 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 820 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 821 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 822 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 823 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 824 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 825 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 826 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 827 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 828 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Sequences P_tetraurelia-Sample_99_60aa-ORF_renamed_min100aa_ORF and P_tetraurelia-Sample_A_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_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_Indo1-7I_60aa-ORF_renamed_min100aa_ORF are exactly identical IMPORTANT WARNING: Sequences P_sexaurelia-Sample_134_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_137_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. IMPORTANT WARNING Found 69 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 nad5.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 572 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 21.19% 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: 572 Name: No Name Provided DataType: AA Substitution Matrix: GTR Using empirical base frequencies RAxML was called as follows: raxml -f a -s nad5.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad5.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 211.708328 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 13.545955 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.170952 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Time for BS model parameter optimization 24.982220 Bootstrap[0]: Time 27.791129 seconds, bootstrap likelihood -10214.567489, best rearrangement setting 13 Bootstrap[1]: Time 2.416099 seconds, bootstrap likelihood -10549.418755, best rearrangement setting 13 Bootstrap[2]: Time 2.613685 seconds, bootstrap likelihood -10228.947022, best rearrangement setting 12 Bootstrap[3]: Time 2.099678 seconds, bootstrap likelihood -10061.694262, best rearrangement setting 15 Bootstrap[4]: Time 2.330967 seconds, bootstrap likelihood -10239.404683, best rearrangement setting 10 Bootstrap[5]: Time 2.130602 seconds, bootstrap likelihood -10419.668449, best rearrangement setting 10 Bootstrap[6]: Time 2.231003 seconds, bootstrap likelihood -11114.338071, best rearrangement setting 6 Bootstrap[7]: Time 2.392895 seconds, bootstrap likelihood -10375.228146, best rearrangement setting 14 Bootstrap[8]: Time 2.296332 seconds, bootstrap likelihood -10754.350109, best rearrangement setting 5 Bootstrap[9]: Time 2.016287 seconds, bootstrap likelihood -10485.260645, best rearrangement setting 7 Bootstrap[10]: Time 2.257721 seconds, bootstrap likelihood -10409.630798, best rearrangement setting 7 Bootstrap[11]: Time 2.001687 seconds, bootstrap likelihood -10857.513930, best rearrangement setting 5 Bootstrap[12]: Time 2.042075 seconds, bootstrap likelihood -10370.631443, best rearrangement setting 8 Bootstrap[13]: Time 2.342796 seconds, bootstrap likelihood -9949.215735, best rearrangement setting 7 Bootstrap[14]: Time 2.478853 seconds, bootstrap likelihood -10631.035453, best rearrangement setting 12 Bootstrap[15]: Time 2.617618 seconds, bootstrap likelihood -10030.422456, best rearrangement setting 15 Bootstrap[16]: Time 2.499775 seconds, bootstrap likelihood -9981.620953, best rearrangement setting 12 Bootstrap[17]: Time 2.188907 seconds, bootstrap likelihood -10201.923541, best rearrangement setting 12 Bootstrap[18]: Time 2.121429 seconds, bootstrap likelihood -10582.327012, best rearrangement setting 5 Bootstrap[19]: Time 2.034719 seconds, bootstrap likelihood -9788.864326, best rearrangement setting 8 Bootstrap[20]: Time 2.852008 seconds, bootstrap likelihood -10350.733845, best rearrangement setting 10 Bootstrap[21]: Time 2.213586 seconds, bootstrap likelihood -10306.377907, best rearrangement setting 6 Bootstrap[22]: Time 2.404236 seconds, bootstrap likelihood -9967.240874, best rearrangement setting 5 Bootstrap[23]: Time 2.733669 seconds, bootstrap likelihood -10507.623454, best rearrangement setting 7 Bootstrap[24]: Time 1.972330 seconds, bootstrap likelihood -10428.348887, best rearrangement setting 8 Bootstrap[25]: Time 2.078526 seconds, bootstrap likelihood -10291.170047, best rearrangement setting 6 Bootstrap[26]: Time 2.546817 seconds, bootstrap likelihood -11073.788155, best rearrangement setting 12 Bootstrap[27]: Time 2.123528 seconds, bootstrap likelihood -10608.655316, best rearrangement setting 10 Bootstrap[28]: Time 2.499561 seconds, bootstrap likelihood -10580.664488, best rearrangement setting 11 Bootstrap[29]: Time 2.437172 seconds, bootstrap likelihood -10068.421485, best rearrangement setting 12 Bootstrap[30]: Time 2.588391 seconds, bootstrap likelihood -10582.740033, best rearrangement setting 15 Bootstrap[31]: Time 2.198150 seconds, bootstrap likelihood -10545.171004, best rearrangement setting 15 Bootstrap[32]: Time 2.336242 seconds, bootstrap likelihood -10692.745107, best rearrangement setting 6 Bootstrap[33]: Time 2.422321 seconds, bootstrap likelihood -10588.031499, best rearrangement setting 15 Bootstrap[34]: Time 1.910487 seconds, bootstrap likelihood -10474.716547, best rearrangement setting 11 Bootstrap[35]: Time 2.405906 seconds, bootstrap likelihood -10352.651375, best rearrangement setting 8 Bootstrap[36]: Time 2.639665 seconds, bootstrap likelihood -10588.199558, best rearrangement setting 9 Bootstrap[37]: Time 2.012784 seconds, bootstrap likelihood -10671.083249, best rearrangement setting 11 Bootstrap[38]: Time 2.194000 seconds, bootstrap likelihood -10591.104356, best rearrangement setting 8 Bootstrap[39]: Time 2.403588 seconds, bootstrap likelihood -10550.708673, best rearrangement setting 13 Bootstrap[40]: Time 2.138436 seconds, bootstrap likelihood -10317.281898, best rearrangement setting 13 Bootstrap[41]: Time 2.445327 seconds, bootstrap likelihood -10375.121308, best rearrangement setting 10 Bootstrap[42]: Time 2.217764 seconds, bootstrap likelihood -10277.294580, best rearrangement setting 5 Bootstrap[43]: Time 2.151468 seconds, bootstrap likelihood -10471.631431, best rearrangement setting 14 Bootstrap[44]: Time 2.472603 seconds, bootstrap likelihood -9810.082356, best rearrangement setting 10 Bootstrap[45]: Time 2.401670 seconds, bootstrap likelihood -10613.088279, best rearrangement setting 15 Bootstrap[46]: Time 2.489466 seconds, bootstrap likelihood -10066.001005, best rearrangement setting 14 Bootstrap[47]: Time 2.158065 seconds, bootstrap likelihood -10915.814966, best rearrangement setting 8 Bootstrap[48]: Time 2.108685 seconds, bootstrap likelihood -11255.912901, best rearrangement setting 6 Bootstrap[49]: Time 2.784771 seconds, bootstrap likelihood -10788.471810, best rearrangement setting 7 Bootstrap[50]: Time 2.250282 seconds, bootstrap likelihood -10631.395882, best rearrangement setting 7 Bootstrap[51]: Time 2.608593 seconds, bootstrap likelihood -10604.946959, best rearrangement setting 11 Bootstrap[52]: Time 2.163532 seconds, bootstrap likelihood -10354.775231, best rearrangement setting 12 Bootstrap[53]: Time 2.270885 seconds, bootstrap likelihood -10022.738428, best rearrangement setting 8 Bootstrap[54]: Time 2.011751 seconds, bootstrap likelihood -11012.533941, best rearrangement setting 9 Bootstrap[55]: Time 2.318725 seconds, bootstrap likelihood -10602.692132, best rearrangement setting 11 Bootstrap[56]: Time 2.422148 seconds, bootstrap likelihood -10524.781957, best rearrangement setting 5 Bootstrap[57]: Time 2.062851 seconds, bootstrap likelihood -10853.790240, best rearrangement setting 7 Bootstrap[58]: Time 2.558876 seconds, bootstrap likelihood -10530.679610, best rearrangement setting 10 Bootstrap[59]: Time 2.507596 seconds, bootstrap likelihood -10603.015337, best rearrangement setting 9 Bootstrap[60]: Time 2.592355 seconds, bootstrap likelihood -10060.782765, best rearrangement setting 7 Bootstrap[61]: Time 2.222256 seconds, bootstrap likelihood -10437.879395, best rearrangement setting 5 Bootstrap[62]: Time 2.506858 seconds, bootstrap likelihood -10374.160692, best rearrangement setting 11 Bootstrap[63]: Time 2.415028 seconds, bootstrap likelihood -10192.877389, best rearrangement setting 12 Bootstrap[64]: Time 2.511967 seconds, bootstrap likelihood -11036.819898, best rearrangement setting 7 Bootstrap[65]: Time 2.266669 seconds, bootstrap likelihood -10582.789018, best rearrangement setting 5 Bootstrap[66]: Time 2.220659 seconds, bootstrap likelihood -10127.450111, best rearrangement setting 5 Bootstrap[67]: Time 2.278298 seconds, bootstrap likelihood -10690.860491, best rearrangement setting 15 Bootstrap[68]: Time 2.731600 seconds, bootstrap likelihood -10043.600060, best rearrangement setting 11 Bootstrap[69]: Time 2.267186 seconds, bootstrap likelihood -10052.702430, best rearrangement setting 5 Bootstrap[70]: Time 2.506105 seconds, bootstrap likelihood -10587.706690, best rearrangement setting 8 Bootstrap[71]: Time 2.718335 seconds, bootstrap likelihood -10289.837381, best rearrangement setting 10 Bootstrap[72]: Time 2.740215 seconds, bootstrap likelihood -10203.158367, best rearrangement setting 11 Bootstrap[73]: Time 2.085911 seconds, bootstrap likelihood -10726.646121, best rearrangement setting 9 Bootstrap[74]: Time 2.315395 seconds, bootstrap likelihood -10634.285324, best rearrangement setting 5 Bootstrap[75]: Time 2.711308 seconds, bootstrap likelihood -10279.053064, best rearrangement setting 8 Bootstrap[76]: Time 2.405456 seconds, bootstrap likelihood -10704.674604, best rearrangement setting 9 Bootstrap[77]: Time 2.189234 seconds, bootstrap likelihood -10438.107967, best rearrangement setting 11 Bootstrap[78]: Time 1.990936 seconds, bootstrap likelihood -10710.286324, best rearrangement setting 15 Bootstrap[79]: Time 2.072269 seconds, bootstrap likelihood -10268.182002, best rearrangement setting 9 Bootstrap[80]: Time 2.290231 seconds, bootstrap likelihood -10743.037730, best rearrangement setting 15 Bootstrap[81]: Time 2.171508 seconds, bootstrap likelihood -10807.396647, best rearrangement setting 7 Bootstrap[82]: Time 1.914712 seconds, bootstrap likelihood -10443.776179, best rearrangement setting 6 Bootstrap[83]: Time 2.124946 seconds, bootstrap likelihood -10799.988370, best rearrangement setting 10 Bootstrap[84]: Time 2.081530 seconds, bootstrap likelihood -10742.262410, best rearrangement setting 11 Bootstrap[85]: Time 2.561504 seconds, bootstrap likelihood -10621.164772, best rearrangement setting 8 Bootstrap[86]: Time 2.177446 seconds, bootstrap likelihood -10387.118246, best rearrangement setting 7 Bootstrap[87]: Time 2.401378 seconds, bootstrap likelihood -10057.254474, best rearrangement setting 7 Bootstrap[88]: Time 2.532190 seconds, bootstrap likelihood -10644.254203, best rearrangement setting 12 Bootstrap[89]: Time 2.587039 seconds, bootstrap likelihood -10062.477119, best rearrangement setting 10 Bootstrap[90]: Time 2.394943 seconds, bootstrap likelihood -10302.527012, best rearrangement setting 8 Bootstrap[91]: Time 2.272141 seconds, bootstrap likelihood -10876.002236, best rearrangement setting 12 Bootstrap[92]: Time 2.412893 seconds, bootstrap likelihood -11071.942215, best rearrangement setting 13 Bootstrap[93]: Time 2.109517 seconds, bootstrap likelihood -10660.031000, best rearrangement setting 15 Bootstrap[94]: Time 2.123853 seconds, bootstrap likelihood -10381.227472, best rearrangement setting 5 Bootstrap[95]: Time 2.363896 seconds, bootstrap likelihood -10095.581295, best rearrangement setting 5 Bootstrap[96]: Time 2.155378 seconds, bootstrap likelihood -9920.233221, best rearrangement setting 13 Bootstrap[97]: Time 2.353702 seconds, bootstrap likelihood -10878.083409, best rearrangement setting 11 Bootstrap[98]: Time 2.462044 seconds, bootstrap likelihood -10706.119172, best rearrangement setting 6 Bootstrap[99]: Time 2.577866 seconds, bootstrap likelihood -10677.060612, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 258.449455 seconds Average Time per Rapid Bootstrap 2.584495 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 213.938894 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 13.467183 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.152650 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.122077 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.017116 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 210.462090 seconds Printed linked AA GTR matrix that achieved an overall improvement of 211.712081 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 12.903191 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.060195 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.106503 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.014008 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Slow ML Search 0 Likelihood: -10480.995500 Slow ML Search 1 Likelihood: -10480.995499 Slow ML Search 2 Likelihood: -10480.995500 Slow ML Search 3 Likelihood: -10480.995500 Slow ML Search 4 Likelihood: -10480.995500 Slow ML Search 5 Likelihood: -10480.995500 Slow ML Search 6 Likelihood: -10480.995500 Slow ML Search 7 Likelihood: -10480.995500 Slow ML Search 8 Likelihood: -10480.995500 Slow ML Search 9 Likelihood: -10480.995500 Slow ML optimization finished Slow ML search Time: 115.690569 seconds Printed linked AA GTR matrix that achieved an overall improvement of 211.708282 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 12.909111 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.060523 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.104470 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.013487 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-nad5.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Thorough ML search Time: 48.393701 seconds Final ML Optimization Likelihood: -10480.996193 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.502454 Tree-Length: 8.497857 rate A <-> R: 0.000000 rate A <-> N: 0.337530 rate A <-> D: 0.000000 rate A <-> C: 3.400004 rate A <-> Q: 0.000000 rate A <-> E: 3.221237 rate A <-> G: 4.098902 rate A <-> H: 0.000000 rate A <-> I: 2.084079 rate A <-> L: 0.645152 rate A <-> K: 0.000000 rate A <-> M: 0.000000 rate A <-> F: 1.092457 rate A <-> P: 5.575309 rate A <-> S: 13.159110 rate A <-> T: 13.294202 rate A <-> W: 0.000000 rate A <-> Y: 0.000000 rate A <-> V: 11.026399 rate R <-> N: 0.000000 rate R <-> D: 0.000000 rate R <-> C: 0.000000 rate R <-> Q: 5.824783 rate R <-> E: 0.000000 rate R <-> G: 0.000000 rate R <-> H: 0.000000 rate R <-> I: 0.000000 rate R <-> L: 0.461159 rate R <-> K: 32.260505 rate R <-> M: 0.000000 rate R <-> F: 0.000000 rate R <-> P: 0.000000 rate R <-> S: 0.862959 rate R <-> T: 0.000000 rate R <-> W: 0.000000 rate R <-> Y: 0.000000 rate R <-> V: 0.000000 rate N <-> D: 20.796485 rate N <-> C: 2.282291 rate N <-> Q: 18.612295 rate N <-> E: 13.268167 rate N <-> G: 0.099075 rate N <-> H: 4.952115 rate N <-> I: 2.717282 rate N <-> L: 0.681452 rate N <-> K: 14.749118 rate N <-> M: 6.252665 rate N <-> F: 0.731465 rate N <-> P: 0.000000 rate N <-> S: 12.057650 rate N <-> T: 8.354477 rate N <-> W: 0.000000 rate N <-> Y: 3.256683 rate N <-> V: 1.774281 rate D <-> C: 0.000000 rate D <-> Q: 0.000000 rate D <-> E: 61.142984 rate D <-> G: 1.648393 rate D <-> H: 0.000000 rate D <-> I: 0.132745 rate D <-> L: 0.143602 rate D <-> K: 0.901093 rate D <-> M: 4.847024 rate D <-> F: 0.000000 rate D <-> P: 0.000000 rate D <-> S: 3.809393 rate D <-> T: 2.662454 rate D <-> W: 2.399534 rate D <-> Y: 0.301553 rate D <-> V: 0.000000 rate C <-> Q: 0.000000 rate C <-> E: 0.000000 rate C <-> G: 2.319052 rate C <-> H: 5.186981 rate C <-> I: 0.000000 rate C <-> L: 0.000000 rate C <-> K: 0.000000 rate C <-> M: 14.886523 rate C <-> F: 3.130399 rate C <-> P: 0.000000 rate C <-> S: 7.569107 rate C <-> T: 0.000000 rate C <-> W: 5.723912 rate C <-> Y: 3.549715 rate C <-> V: 1.454036 rate Q <-> E: 7.103503 rate Q <-> G: 1.310175 rate Q <-> H: 18.381987 rate Q <-> I: 0.000000 rate Q <-> L: 0.000000 rate Q <-> K: 15.459964 rate Q <-> M: 0.000000 rate Q <-> F: 0.985832 rate Q <-> P: 4.484325 rate Q <-> S: 0.000000 rate Q <-> T: 3.406148 rate Q <-> W: 3.396033 rate Q <-> Y: 1.654775 rate Q <-> V: 0.000000 rate E <-> G: 0.000000 rate E <-> H: 0.000000 rate E <-> I: 0.237446 rate E <-> L: 0.652149 rate E <-> K: 6.168784 rate E <-> M: 0.000000 rate E <-> F: 0.000000 rate E <-> P: 5.161460 rate E <-> S: 2.266303 rate E <-> T: 2.252249 rate E <-> W: 0.000000 rate E <-> Y: 2.138902 rate E <-> V: 0.000000 rate G <-> H: 0.000000 rate G <-> I: 0.450972 rate G <-> L: 0.000000 rate G <-> K: 0.000000 rate G <-> M: 0.000000 rate G <-> F: 0.358956 rate G <-> P: 0.000000 rate G <-> S: 4.515466 rate G <-> T: 0.800794 rate G <-> W: 4.338187 rate G <-> Y: 0.000000 rate G <-> V: 0.000000 rate H <-> I: 0.969013 rate H <-> L: 0.000000 rate H <-> K: 0.000000 rate H <-> M: 0.000000 rate H <-> F: 0.703768 rate H <-> P: 0.000000 rate H <-> S: 2.297050 rate H <-> T: 2.703852 rate H <-> W: 0.000000 rate H <-> Y: 12.263159 rate H <-> V: 0.000000 rate I <-> L: 13.984189 rate I <-> K: 0.917558 rate I <-> M: 15.796020 rate I <-> F: 1.698023 rate I <-> P: 0.000000 rate I <-> S: 0.448681 rate I <-> T: 8.102272 rate I <-> W: 0.000000 rate I <-> Y: 1.818739 rate I <-> V: 44.977169 rate L <-> K: 0.975853 rate L <-> M: 25.092498 rate L <-> F: 7.071227 rate L <-> P: 0.593587 rate L <-> S: 1.366124 rate L <-> T: 2.119038 rate L <-> W: 1.309743 rate L <-> Y: 0.758364 rate L <-> V: 6.638178 rate K <-> M: 0.000000 rate K <-> F: 0.000000 rate K <-> P: 0.000000 rate K <-> S: 1.020651 rate K <-> T: 0.989442 rate K <-> W: 1.954478 rate K <-> Y: 2.099582 rate K <-> V: 0.000000 rate M <-> F: 1.387313 rate M <-> P: 0.000000 rate M <-> S: 0.000000 rate M <-> T: 16.607398 rate M <-> W: 0.389596 rate M <-> Y: 0.000000 rate M <-> V: 28.461703 rate F <-> P: 0.000000 rate F <-> S: 1.196038 rate F <-> T: 1.644113 rate F <-> W: 1.914422 rate F <-> Y: 7.234349 rate F <-> V: 2.238865 rate P <-> S: 3.883601 rate P <-> T: 3.162245 rate P <-> W: 0.000000 rate P <-> Y: 2.679216 rate P <-> V: 2.238815 rate S <-> T: 18.047140 rate S <-> W: 0.000000 rate S <-> Y: 1.840214 rate S <-> V: 2.063056 rate T <-> W: 0.000000 rate T <-> Y: 0.961757 rate T <-> V: 12.793278 rate W <-> Y: 6.805019 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.057540 freq pi(R): 0.017044 freq pi(N): 0.054660 freq pi(D): 0.024288 freq pi(C): 0.014675 freq pi(Q): 0.010681 freq pi(E): 0.018762 freq pi(G): 0.037245 freq pi(H): 0.011703 freq pi(I): 0.096178 freq pi(L): 0.145637 freq pi(K): 0.043561 freq pi(M): 0.012307 freq pi(F): 0.153949 freq pi(P): 0.015093 freq pi(S): 0.105744 freq pi(T): 0.048484 freq pi(W): 0.012028 freq pi(Y): 0.067199 freq pi(V): 0.053221 ML search took 374.651520 secs or 0.104070 hours Combined Bootstrap and ML search took 633.102148 secs or 0.175862 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-nad5.renamed.muscle.Oligohymenophorea Found 1 tree in File /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-nad5.renamed.muscle.Oligohymenophorea Program execution info written to /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-nad5.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-nad5.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-nad5.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-nad5.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-nad5.renamed.muscle.Oligohymenophorea Overall execution time for full ML analysis: 633.118261 secs or 0.175866 hours or 0.007328 days