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_Indo1-7I_60aa-ORF_renamed_min100aa_ORF are exactly identical 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_131_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_127_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_137_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_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 9 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 rps3.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 315 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 55.20% 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: 315 Name: No Name Provided DataType: AA Substitution Matrix: GTR Using empirical base frequencies RAxML was called as follows: raxml -f a -s rps3.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-rps3.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 155.309788 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 9.689885 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.611680 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Time for BS model parameter optimization 18.703884 Bootstrap[0]: Time 20.684893 seconds, bootstrap likelihood -4550.125052, best rearrangement setting 13 Bootstrap[1]: Time 1.603940 seconds, bootstrap likelihood -4570.905190, best rearrangement setting 13 Bootstrap[2]: Time 1.631294 seconds, bootstrap likelihood -4589.582606, best rearrangement setting 12 Bootstrap[3]: Time 1.774935 seconds, bootstrap likelihood -4634.589047, best rearrangement setting 15 Bootstrap[4]: Time 1.676514 seconds, bootstrap likelihood -4495.749063, best rearrangement setting 10 Bootstrap[5]: Time 1.855190 seconds, bootstrap likelihood -4493.421963, best rearrangement setting 10 Bootstrap[6]: Time 1.418877 seconds, bootstrap likelihood -4570.623427, best rearrangement setting 6 Bootstrap[7]: Time 1.552557 seconds, bootstrap likelihood -4790.227018, best rearrangement setting 14 Bootstrap[8]: Time 1.929799 seconds, bootstrap likelihood -4046.810018, best rearrangement setting 5 Bootstrap[9]: Time 1.424117 seconds, bootstrap likelihood -4540.026391, best rearrangement setting 7 Bootstrap[10]: Time 1.512902 seconds, bootstrap likelihood -4586.991180, best rearrangement setting 7 Bootstrap[11]: Time 1.689040 seconds, bootstrap likelihood -4300.295655, best rearrangement setting 5 Bootstrap[12]: Time 1.839163 seconds, bootstrap likelihood -4552.390759, best rearrangement setting 8 Bootstrap[13]: Time 1.961422 seconds, bootstrap likelihood -4335.676246, best rearrangement setting 7 Bootstrap[14]: Time 1.585413 seconds, bootstrap likelihood -4535.438383, best rearrangement setting 12 Bootstrap[15]: Time 1.707802 seconds, bootstrap likelihood -4544.891994, best rearrangement setting 15 Bootstrap[16]: Time 1.672597 seconds, bootstrap likelihood -4136.163379, best rearrangement setting 12 Bootstrap[17]: Time 1.661450 seconds, bootstrap likelihood -4348.775820, best rearrangement setting 12 Bootstrap[18]: Time 1.601887 seconds, bootstrap likelihood -4625.364546, best rearrangement setting 5 Bootstrap[19]: Time 1.604092 seconds, bootstrap likelihood -4930.775222, best rearrangement setting 8 Bootstrap[20]: Time 1.502721 seconds, bootstrap likelihood -4682.867926, best rearrangement setting 10 Bootstrap[21]: Time 1.480243 seconds, bootstrap likelihood -4406.290432, best rearrangement setting 6 Bootstrap[22]: Time 1.986968 seconds, bootstrap likelihood -4475.161391, best rearrangement setting 5 Bootstrap[23]: Time 1.892531 seconds, bootstrap likelihood -4612.636869, best rearrangement setting 7 Bootstrap[24]: Time 2.068113 seconds, bootstrap likelihood -4050.210658, best rearrangement setting 8 Bootstrap[25]: Time 1.706075 seconds, bootstrap likelihood -4397.107860, best rearrangement setting 6 Bootstrap[26]: Time 1.753847 seconds, bootstrap likelihood -4230.505014, best rearrangement setting 12 Bootstrap[27]: Time 1.751443 seconds, bootstrap likelihood -4583.973997, best rearrangement setting 10 Bootstrap[28]: Time 1.605704 seconds, bootstrap likelihood -4367.128468, best rearrangement setting 11 Bootstrap[29]: Time 1.938558 seconds, bootstrap likelihood -4430.969960, best rearrangement setting 12 Bootstrap[30]: Time 1.540103 seconds, bootstrap likelihood -4618.076693, best rearrangement setting 15 Bootstrap[31]: Time 1.850860 seconds, bootstrap likelihood -4380.726041, best rearrangement setting 15 Bootstrap[32]: Time 1.483247 seconds, bootstrap likelihood -4536.379806, best rearrangement setting 6 Bootstrap[33]: Time 2.013732 seconds, bootstrap likelihood -4401.133116, best rearrangement setting 15 Bootstrap[34]: Time 1.925527 seconds, bootstrap likelihood -4341.447612, best rearrangement setting 11 Bootstrap[35]: Time 1.652785 seconds, bootstrap likelihood -4505.886803, best rearrangement setting 8 Bootstrap[36]: Time 1.738916 seconds, bootstrap likelihood -4346.390844, best rearrangement setting 9 Bootstrap[37]: Time 1.525953 seconds, bootstrap likelihood -4739.926104, best rearrangement setting 11 Bootstrap[38]: Time 1.975672 seconds, bootstrap likelihood -4800.027720, best rearrangement setting 8 Bootstrap[39]: Time 1.788235 seconds, bootstrap likelihood -4611.596194, best rearrangement setting 13 Bootstrap[40]: Time 1.854149 seconds, bootstrap likelihood -4137.786850, best rearrangement setting 13 Bootstrap[41]: Time 1.933452 seconds, bootstrap likelihood -4503.913975, best rearrangement setting 10 Bootstrap[42]: Time 1.885509 seconds, bootstrap likelihood -4615.147396, best rearrangement setting 5 Bootstrap[43]: Time 1.816997 seconds, bootstrap likelihood -4611.298281, best rearrangement setting 14 Bootstrap[44]: Time 1.799799 seconds, bootstrap likelihood -4515.886622, best rearrangement setting 10 Bootstrap[45]: Time 1.568490 seconds, bootstrap likelihood -4364.233357, best rearrangement setting 15 Bootstrap[46]: Time 1.782066 seconds, bootstrap likelihood -4651.780825, best rearrangement setting 14 Bootstrap[47]: Time 1.794400 seconds, bootstrap likelihood -4646.773853, best rearrangement setting 8 Bootstrap[48]: Time 1.600852 seconds, bootstrap likelihood -4463.168551, best rearrangement setting 6 Bootstrap[49]: Time 1.734318 seconds, bootstrap likelihood -4660.976752, best rearrangement setting 7 Bootstrap[50]: Time 1.587605 seconds, bootstrap likelihood -4306.423072, best rearrangement setting 7 Bootstrap[51]: Time 1.648652 seconds, bootstrap likelihood -4481.597956, best rearrangement setting 11 Bootstrap[52]: Time 1.575872 seconds, bootstrap likelihood -4466.462264, best rearrangement setting 12 Bootstrap[53]: Time 1.764085 seconds, bootstrap likelihood -4500.967025, best rearrangement setting 8 Bootstrap[54]: Time 1.573466 seconds, bootstrap likelihood -4307.886509, best rearrangement setting 9 Bootstrap[55]: Time 1.811820 seconds, bootstrap likelihood -4389.601547, best rearrangement setting 11 Bootstrap[56]: Time 1.805939 seconds, bootstrap likelihood -4830.452734, best rearrangement setting 5 Bootstrap[57]: Time 2.055936 seconds, bootstrap likelihood -4936.256711, best rearrangement setting 7 Bootstrap[58]: Time 1.601713 seconds, bootstrap likelihood -4728.776646, best rearrangement setting 10 Bootstrap[59]: Time 1.747818 seconds, bootstrap likelihood -4212.618160, best rearrangement setting 9 Bootstrap[60]: Time 1.714581 seconds, bootstrap likelihood -4271.546336, best rearrangement setting 7 Bootstrap[61]: Time 1.846930 seconds, bootstrap likelihood -4595.465972, best rearrangement setting 5 Bootstrap[62]: Time 1.723864 seconds, bootstrap likelihood -4577.514142, best rearrangement setting 11 Bootstrap[63]: Time 1.648514 seconds, bootstrap likelihood -4921.105161, best rearrangement setting 12 Bootstrap[64]: Time 1.884986 seconds, bootstrap likelihood -4419.174391, best rearrangement setting 7 Bootstrap[65]: Time 1.430830 seconds, bootstrap likelihood -4587.006423, best rearrangement setting 5 Bootstrap[66]: Time 1.778106 seconds, bootstrap likelihood -4404.346233, best rearrangement setting 5 Bootstrap[67]: Time 1.541213 seconds, bootstrap likelihood -4902.780089, best rearrangement setting 15 Bootstrap[68]: Time 2.012021 seconds, bootstrap likelihood -4590.734404, best rearrangement setting 11 Bootstrap[69]: Time 1.563047 seconds, bootstrap likelihood -4274.146872, best rearrangement setting 5 Bootstrap[70]: Time 1.768732 seconds, bootstrap likelihood -4404.409063, best rearrangement setting 8 Bootstrap[71]: Time 1.689562 seconds, bootstrap likelihood -4760.282177, best rearrangement setting 10 Bootstrap[72]: Time 1.603028 seconds, bootstrap likelihood -4110.275864, best rearrangement setting 11 Bootstrap[73]: Time 2.119558 seconds, bootstrap likelihood -4490.534427, best rearrangement setting 9 Bootstrap[74]: Time 1.826042 seconds, bootstrap likelihood -4538.175478, best rearrangement setting 5 Bootstrap[75]: Time 1.658484 seconds, bootstrap likelihood -4552.257421, best rearrangement setting 8 Bootstrap[76]: Time 1.478701 seconds, bootstrap likelihood -4558.625446, best rearrangement setting 9 Bootstrap[77]: Time 1.865332 seconds, bootstrap likelihood -4431.276600, best rearrangement setting 11 Bootstrap[78]: Time 1.939084 seconds, bootstrap likelihood -4238.985960, best rearrangement setting 15 Bootstrap[79]: Time 1.611635 seconds, bootstrap likelihood -4646.862556, best rearrangement setting 9 Bootstrap[80]: Time 1.780371 seconds, bootstrap likelihood -4819.217563, best rearrangement setting 15 Bootstrap[81]: Time 1.872454 seconds, bootstrap likelihood -4627.391096, best rearrangement setting 7 Bootstrap[82]: Time 1.880625 seconds, bootstrap likelihood -4512.006260, best rearrangement setting 6 Bootstrap[83]: Time 1.980821 seconds, bootstrap likelihood -4412.554980, best rearrangement setting 10 Bootstrap[84]: Time 1.696588 seconds, bootstrap likelihood -4695.500632, best rearrangement setting 11 Bootstrap[85]: Time 2.307386 seconds, bootstrap likelihood -4617.349681, best rearrangement setting 8 Bootstrap[86]: Time 1.564372 seconds, bootstrap likelihood -4436.455977, best rearrangement setting 7 Bootstrap[87]: Time 1.826751 seconds, bootstrap likelihood -4749.723624, best rearrangement setting 7 Bootstrap[88]: Time 1.749449 seconds, bootstrap likelihood -4269.156320, best rearrangement setting 12 Bootstrap[89]: Time 1.983406 seconds, bootstrap likelihood -4495.873665, best rearrangement setting 10 Bootstrap[90]: Time 1.643424 seconds, bootstrap likelihood -4857.036313, best rearrangement setting 8 Bootstrap[91]: Time 2.041930 seconds, bootstrap likelihood -4533.183806, best rearrangement setting 12 Bootstrap[92]: Time 1.904667 seconds, bootstrap likelihood -4372.729573, best rearrangement setting 13 Bootstrap[93]: Time 1.438169 seconds, bootstrap likelihood -4575.927955, best rearrangement setting 15 Bootstrap[94]: Time 1.878284 seconds, bootstrap likelihood -4199.894394, best rearrangement setting 5 Bootstrap[95]: Time 1.724285 seconds, bootstrap likelihood -4645.027672, best rearrangement setting 5 Bootstrap[96]: Time 1.557478 seconds, bootstrap likelihood -5135.416159, best rearrangement setting 13 Bootstrap[97]: Time 1.683858 seconds, bootstrap likelihood -4854.494716, best rearrangement setting 11 Bootstrap[98]: Time 1.929400 seconds, bootstrap likelihood -4737.429312, best rearrangement setting 6 Bootstrap[99]: Time 1.960238 seconds, bootstrap likelihood -4437.417490, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 193.711776 seconds Average Time per Rapid Bootstrap 1.937118 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 152.560439 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 10.151464 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.856894 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.096798 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 125.340915 seconds Printed linked AA GTR matrix that achieved an overall improvement of 157.013759 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 10.929070 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.877506 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.096813 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Slow ML Search 0 Likelihood: -4542.065156 Slow ML Search 1 Likelihood: -4542.065156 Slow ML Search 2 Likelihood: -4542.065156 Slow ML Search 3 Likelihood: -4542.065156 Slow ML Search 4 Likelihood: -4542.065156 Slow ML Search 5 Likelihood: -4542.065158 Slow ML Search 6 Likelihood: -4542.065158 Slow ML Search 7 Likelihood: -4542.065158 Slow ML Search 8 Likelihood: -4542.065158 Slow ML Search 9 Likelihood: -4542.066898 Slow ML optimization finished Slow ML search Time: 82.610867 seconds Printed linked AA GTR matrix that achieved an overall improvement of 157.024587 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 10.942821 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.879104 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.097133 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-rps3.renamed.muscle.Oligohymenophorea_Partition_No Name Provided Thorough ML search Time: 29.502706 seconds Final ML Optimization Likelihood: -4542.075789 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 1.187906 Tree-Length: 14.664210 rate A <-> R: 0.000000 rate A <-> N: 4.140739 rate A <-> D: 5.290352 rate A <-> C: 0.000000 rate A <-> Q: 8.389301 rate A <-> E: 3.558192 rate A <-> G: 5.594459 rate A <-> H: 0.000000 rate A <-> I: 4.995717 rate A <-> L: 0.834459 rate A <-> K: 0.000000 rate A <-> M: 0.000000 rate A <-> F: 4.192045 rate A <-> P: 43.756049 rate A <-> S: 9.116749 rate A <-> T: 23.765921 rate A <-> W: 0.000000 rate A <-> Y: 0.000000 rate A <-> V: 39.275819 rate R <-> N: 0.160676 rate R <-> D: 0.000000 rate R <-> C: 4.812044 rate R <-> Q: 4.840113 rate R <-> E: 0.969132 rate R <-> G: 0.000000 rate R <-> H: 0.000000 rate R <-> I: 3.018340 rate R <-> L: 1.851703 rate R <-> K: 30.264114 rate R <-> M: 0.000000 rate R <-> F: 0.000000 rate R <-> P: 0.000000 rate R <-> S: 3.304834 rate R <-> T: 0.000000 rate R <-> W: 0.000000 rate R <-> Y: 0.000000 rate R <-> V: 0.000000 rate N <-> D: 10.565417 rate N <-> C: 0.000000 rate N <-> Q: 5.360897 rate N <-> E: 2.017874 rate N <-> G: 2.946964 rate N <-> H: 26.157720 rate N <-> I: 0.432101 rate N <-> L: 0.000000 rate N <-> K: 8.154650 rate N <-> M: 0.000000 rate N <-> F: 1.026345 rate N <-> P: 0.000000 rate N <-> S: 17.125685 rate N <-> T: 12.635550 rate N <-> W: 0.000000 rate N <-> Y: 1.198366 rate N <-> V: 0.820593 rate D <-> C: 0.000000 rate D <-> Q: 0.000000 rate D <-> E: 14.326635 rate D <-> G: 12.631090 rate D <-> H: 6.782266 rate D <-> I: 0.218585 rate D <-> L: 0.341116 rate D <-> K: 0.804634 rate D <-> M: 0.000000 rate D <-> F: 0.000000 rate D <-> P: 0.000000 rate D <-> S: 3.541781 rate D <-> T: 1.676598 rate D <-> W: 0.000000 rate D <-> Y: 0.217937 rate D <-> V: 0.883118 rate C <-> Q: 0.000000 rate C <-> E: 0.000000 rate C <-> G: 0.000000 rate C <-> H: 0.000000 rate C <-> I: 2.313218 rate C <-> L: 0.000000 rate C <-> K: 0.000000 rate C <-> M: 0.000000 rate C <-> F: 0.000000 rate C <-> P: 0.000000 rate C <-> S: 3.811445 rate C <-> T: 0.000000 rate C <-> W: 0.000000 rate C <-> Y: 2.235036 rate C <-> V: 3.256162 rate Q <-> E: 2.371758 rate Q <-> G: 0.000000 rate Q <-> H: 71.338549 rate Q <-> I: 0.000000 rate Q <-> L: 1.358542 rate Q <-> K: 2.929110 rate Q <-> M: 11.630304 rate Q <-> F: 0.000000 rate Q <-> P: 0.000000 rate Q <-> S: 0.000000 rate Q <-> T: 0.000000 rate Q <-> W: 0.000000 rate Q <-> Y: 1.802619 rate Q <-> V: 1.926107 rate E <-> G: 1.995290 rate E <-> H: 7.874654 rate E <-> I: 0.381439 rate E <-> L: 0.470719 rate E <-> K: 1.423726 rate E <-> M: 0.000000 rate E <-> F: 0.000000 rate E <-> P: 3.105138 rate E <-> S: 0.000000 rate E <-> T: 4.244575 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: 0.381976 rate G <-> P: 0.000000 rate G <-> S: 4.802241 rate G <-> T: 0.000000 rate G <-> W: 0.000000 rate G <-> Y: 0.000000 rate G <-> V: 4.917251 rate H <-> I: 1.422643 rate H <-> L: 0.000000 rate H <-> K: 0.000000 rate H <-> M: 0.000000 rate H <-> F: 5.184000 rate H <-> P: 0.000000 rate H <-> S: 21.310988 rate H <-> T: 0.000000 rate H <-> W: 0.000000 rate H <-> Y: 56.253467 rate H <-> V: 0.000000 rate I <-> L: 12.964713 rate I <-> K: 0.000000 rate I <-> M: 10.868196 rate I <-> F: 2.882553 rate I <-> P: 0.000000 rate I <-> S: 0.000000 rate I <-> T: 17.734461 rate I <-> W: 0.000000 rate I <-> Y: 0.000000 rate I <-> V: 75.890067 rate L <-> K: 0.961771 rate L <-> M: 27.358607 rate L <-> F: 6.281688 rate L <-> P: 10.021797 rate L <-> S: 2.128877 rate L <-> T: 3.946115 rate L <-> W: 0.877161 rate L <-> Y: 1.910669 rate L <-> V: 3.129411 rate K <-> M: 3.840403 rate K <-> F: 0.000000 rate K <-> P: 8.092670 rate K <-> S: 0.788572 rate K <-> T: 1.933728 rate K <-> W: 0.000000 rate K <-> Y: 0.397478 rate K <-> V: 0.000000 rate M <-> F: 4.784090 rate M <-> P: 0.000000 rate M <-> S: 0.000000 rate M <-> T: 0.000000 rate M <-> W: 0.000000 rate M <-> Y: 0.000000 rate M <-> V: 0.000000 rate F <-> P: 0.710844 rate F <-> S: 2.033127 rate F <-> T: 0.000000 rate F <-> W: 0.000000 rate F <-> Y: 10.349744 rate F <-> V: 2.446603 rate P <-> S: 25.921898 rate P <-> T: 9.686441 rate P <-> W: 0.000000 rate P <-> Y: 0.000000 rate P <-> V: 0.000000 rate S <-> T: 37.379874 rate S <-> W: 0.487863 rate S <-> Y: 2.635639 rate S <-> V: 0.962532 rate T <-> W: 0.000000 rate T <-> Y: 1.212511 rate T <-> V: 4.667733 rate W <-> Y: 0.958126 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.031197 freq pi(R): 0.023506 freq pi(N): 0.078350 freq pi(D): 0.077013 freq pi(C): 0.011968 freq pi(Q): 0.026850 freq pi(E): 0.091894 freq pi(G): 0.027686 freq pi(H): 0.008290 freq pi(I): 0.054272 freq pi(L): 0.096576 freq pi(K): 0.105104 freq pi(M): 0.010965 freq pi(F): 0.099084 freq pi(P): 0.007788 freq pi(S): 0.083701 freq pi(T): 0.031866 freq pi(W): 0.026515 freq pi(Y): 0.062465 freq pi(V): 0.044908 ML search took 237.586161 secs or 0.065996 hours Combined Bootstrap and ML search took 431.298787 secs or 0.119805 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-rps3.renamed.muscle.Oligohymenophorea Found 1 tree in File /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-rps3.renamed.muscle.Oligohymenophorea Program execution info written to /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-rps3.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-rps3.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-rps3.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-rps3.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-rps3.renamed.muscle.Oligohymenophorea Overall execution time for full ML analysis: 431.316755 secs or 0.119810 hours or 0.004992 days