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 8557 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 15.02% 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 ML estimate of 25 per site rate categories Likelihood of final tree will be evaluated and optimized under GAMMA GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units Partition: 0 Alignment Patterns: 8557 Name: No Name Provided DataType: AA Substitution Matrix: GTR Using empirical base frequencies RAxML was called as follows: raxml -f a -s supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov.fa -n RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov -m PROTCATGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 14928.805043 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2584.727643 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 126.771939 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.094110 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Time for BS model parameter optimization 124.566326 Bootstrap[0]: Time 131.075124 seconds, bootstrap likelihood -151903.387126, best rearrangement setting 13 Bootstrap[1]: Time 5.693349 seconds, bootstrap likelihood -150560.891425, best rearrangement setting 13 Bootstrap[2]: Time 5.855600 seconds, bootstrap likelihood -152298.184519, best rearrangement setting 12 Bootstrap[3]: Time 5.742208 seconds, bootstrap likelihood -154323.534973, best rearrangement setting 15 Bootstrap[4]: Time 6.012138 seconds, bootstrap likelihood -152444.236341, best rearrangement setting 10 Bootstrap[5]: Time 5.544242 seconds, bootstrap likelihood -152523.413272, best rearrangement setting 10 Bootstrap[6]: Time 5.630352 seconds, bootstrap likelihood -153584.574938, best rearrangement setting 6 Bootstrap[7]: Time 5.928924 seconds, bootstrap likelihood -152247.738390, best rearrangement setting 14 Bootstrap[8]: Time 5.734396 seconds, bootstrap likelihood -152146.448284, best rearrangement setting 5 Bootstrap[9]: Time 2.296724 seconds, bootstrap likelihood -154020.459077, best rearrangement setting 7 Bootstrap[10]: Time 6.258711 seconds, bootstrap likelihood -153298.351310, best rearrangement setting 7 Bootstrap[11]: Time 5.792949 seconds, bootstrap likelihood -154286.054621, best rearrangement setting 5 Bootstrap[12]: Time 5.689215 seconds, bootstrap likelihood -153237.435828, best rearrangement setting 8 Bootstrap[13]: Time 5.713978 seconds, bootstrap likelihood -154368.979474, best rearrangement setting 7 Bootstrap[14]: Time 5.782894 seconds, bootstrap likelihood -153980.844721, best rearrangement setting 12 Bootstrap[15]: Time 5.927691 seconds, bootstrap likelihood -154220.321948, best rearrangement setting 15 Bootstrap[16]: Time 5.733738 seconds, bootstrap likelihood -152576.196937, best rearrangement setting 12 Bootstrap[17]: Time 6.258348 seconds, bootstrap likelihood -154058.403763, best rearrangement setting 12 Bootstrap[18]: Time 5.816287 seconds, bootstrap likelihood -152114.340346, best rearrangement setting 5 Bootstrap[19]: Time 5.689344 seconds, bootstrap likelihood -153068.000313, best rearrangement setting 8 Bootstrap[20]: Time 2.568397 seconds, bootstrap likelihood -151824.266460, best rearrangement setting 10 Bootstrap[21]: Time 5.736465 seconds, bootstrap likelihood -153146.079799, best rearrangement setting 6 Bootstrap[22]: Time 5.796177 seconds, bootstrap likelihood -153495.749661, best rearrangement setting 5 Bootstrap[23]: Time 6.156184 seconds, bootstrap likelihood -152602.551844, best rearrangement setting 7 Bootstrap[24]: Time 5.706249 seconds, bootstrap likelihood -153597.654475, best rearrangement setting 8 Bootstrap[25]: Time 5.751416 seconds, bootstrap likelihood -152608.277095, best rearrangement setting 6 Bootstrap[26]: Time 2.446047 seconds, bootstrap likelihood -153885.725633, best rearrangement setting 12 Bootstrap[27]: Time 5.897558 seconds, bootstrap likelihood -152813.347303, best rearrangement setting 10 Bootstrap[28]: Time 5.887736 seconds, bootstrap likelihood -152812.990096, best rearrangement setting 11 Bootstrap[29]: Time 5.522538 seconds, bootstrap likelihood -153497.291296, best rearrangement setting 12 Bootstrap[30]: Time 6.010808 seconds, bootstrap likelihood -154174.631643, best rearrangement setting 15 Bootstrap[31]: Time 5.704114 seconds, bootstrap likelihood -152848.138610, best rearrangement setting 15 Bootstrap[32]: Time 5.767981 seconds, bootstrap likelihood -153913.384626, best rearrangement setting 6 Bootstrap[33]: Time 5.835113 seconds, bootstrap likelihood -152954.287842, best rearrangement setting 15 Bootstrap[34]: Time 5.637768 seconds, bootstrap likelihood -152833.612800, best rearrangement setting 11 Bootstrap[35]: Time 5.736380 seconds, bootstrap likelihood -151741.862030, best rearrangement setting 8 Bootstrap[36]: Time 5.697125 seconds, bootstrap likelihood -151539.580140, best rearrangement setting 9 Bootstrap[37]: Time 5.912132 seconds, bootstrap likelihood -153545.845253, best rearrangement setting 11 Bootstrap[38]: Time 5.899591 seconds, bootstrap likelihood -154119.216907, best rearrangement setting 8 Bootstrap[39]: Time 5.730409 seconds, bootstrap likelihood -154260.175598, best rearrangement setting 13 Bootstrap[40]: Time 2.577442 seconds, bootstrap likelihood -152374.937757, best rearrangement setting 13 Bootstrap[41]: Time 6.012409 seconds, bootstrap likelihood -152622.669947, best rearrangement setting 10 Bootstrap[42]: Time 6.278666 seconds, bootstrap likelihood -154704.118525, best rearrangement setting 5 Bootstrap[43]: Time 5.753190 seconds, bootstrap likelihood -154282.375236, best rearrangement setting 14 Bootstrap[44]: Time 5.852095 seconds, bootstrap likelihood -151248.784047, best rearrangement setting 10 Bootstrap[45]: Time 2.356789 seconds, bootstrap likelihood -153579.988932, best rearrangement setting 15 Bootstrap[46]: Time 5.838509 seconds, bootstrap likelihood -151807.963669, best rearrangement setting 14 Bootstrap[47]: Time 5.645256 seconds, bootstrap likelihood -153686.596746, best rearrangement setting 8 Bootstrap[48]: Time 5.840827 seconds, bootstrap likelihood -153315.140401, best rearrangement setting 6 Bootstrap[49]: Time 5.665054 seconds, bootstrap likelihood -152769.758268, best rearrangement setting 7 Bootstrap[50]: Time 6.257261 seconds, bootstrap likelihood -154550.184788, best rearrangement setting 7 Bootstrap[51]: Time 5.843313 seconds, bootstrap likelihood -153899.325520, best rearrangement setting 11 Bootstrap[52]: Time 6.048991 seconds, bootstrap likelihood -155055.273875, best rearrangement setting 12 Bootstrap[53]: Time 5.756277 seconds, bootstrap likelihood -152407.561625, best rearrangement setting 8 Bootstrap[54]: Time 5.686049 seconds, bootstrap likelihood -152180.318131, best rearrangement setting 9 Bootstrap[55]: Time 5.728220 seconds, bootstrap likelihood -153404.467673, best rearrangement setting 11 Bootstrap[56]: Time 5.632808 seconds, bootstrap likelihood -155578.810019, best rearrangement setting 5 Bootstrap[57]: Time 5.930980 seconds, bootstrap likelihood -152906.111990, best rearrangement setting 7 Bootstrap[58]: Time 5.528245 seconds, bootstrap likelihood -153373.142444, best rearrangement setting 10 Bootstrap[59]: Time 5.886795 seconds, bootstrap likelihood -154639.509295, best rearrangement setting 9 Bootstrap[60]: Time 6.338957 seconds, bootstrap likelihood -152205.845540, best rearrangement setting 7 Bootstrap[61]: Time 2.460783 seconds, bootstrap likelihood -151831.562883, best rearrangement setting 5 Bootstrap[62]: Time 5.719430 seconds, bootstrap likelihood -151597.705709, best rearrangement setting 11 Bootstrap[63]: Time 5.636529 seconds, bootstrap likelihood -153924.723739, best rearrangement setting 12 Bootstrap[64]: Time 6.028899 seconds, bootstrap likelihood -152125.921765, best rearrangement setting 7 Bootstrap[65]: Time 5.543123 seconds, bootstrap likelihood -152801.923878, best rearrangement setting 5 Bootstrap[66]: Time 5.608343 seconds, bootstrap likelihood -152032.621091, best rearrangement setting 5 Bootstrap[67]: Time 5.627700 seconds, bootstrap likelihood -152543.021840, best rearrangement setting 15 Bootstrap[68]: Time 6.007758 seconds, bootstrap likelihood -154130.210802, best rearrangement setting 11 Bootstrap[69]: Time 2.393194 seconds, bootstrap likelihood -153118.882497, best rearrangement setting 5 Bootstrap[70]: Time 5.959809 seconds, bootstrap likelihood -154517.656524, best rearrangement setting 8 Bootstrap[71]: Time 6.002561 seconds, bootstrap likelihood -152580.408907, best rearrangement setting 10 Bootstrap[72]: Time 2.380308 seconds, bootstrap likelihood -154240.892421, best rearrangement setting 11 Bootstrap[73]: Time 2.416047 seconds, bootstrap likelihood -152569.057152, best rearrangement setting 9 Bootstrap[74]: Time 5.693585 seconds, bootstrap likelihood -154027.796999, best rearrangement setting 5 Bootstrap[75]: Time 5.855130 seconds, bootstrap likelihood -152226.038848, best rearrangement setting 8 Bootstrap[76]: Time 5.906850 seconds, bootstrap likelihood -153041.032952, best rearrangement setting 9 Bootstrap[77]: Time 5.750020 seconds, bootstrap likelihood -153123.068825, best rearrangement setting 11 Bootstrap[78]: Time 5.941831 seconds, bootstrap likelihood -153149.027534, best rearrangement setting 15 Bootstrap[79]: Time 5.767446 seconds, bootstrap likelihood -153156.906363, best rearrangement setting 9 Bootstrap[80]: Time 5.993851 seconds, bootstrap likelihood -153740.102426, best rearrangement setting 15 Bootstrap[81]: Time 5.822816 seconds, bootstrap likelihood -154269.662438, best rearrangement setting 7 Bootstrap[82]: Time 5.755653 seconds, bootstrap likelihood -153121.488674, best rearrangement setting 6 Bootstrap[83]: Time 5.731383 seconds, bootstrap likelihood -152521.415203, best rearrangement setting 10 Bootstrap[84]: Time 6.196255 seconds, bootstrap likelihood -152858.789876, best rearrangement setting 11 Bootstrap[85]: Time 5.834025 seconds, bootstrap likelihood -152893.178592, best rearrangement setting 8 Bootstrap[86]: Time 2.465635 seconds, bootstrap likelihood -154082.595744, best rearrangement setting 7 Bootstrap[87]: Time 5.799552 seconds, bootstrap likelihood -152762.135507, best rearrangement setting 7 Bootstrap[88]: Time 5.814361 seconds, bootstrap likelihood -152965.394117, best rearrangement setting 12 Bootstrap[89]: Time 5.695026 seconds, bootstrap likelihood -153910.036528, best rearrangement setting 10 Bootstrap[90]: Time 6.535995 seconds, bootstrap likelihood -154055.613001, best rearrangement setting 8 Bootstrap[91]: Time 6.315619 seconds, bootstrap likelihood -152067.880680, best rearrangement setting 12 Bootstrap[92]: Time 5.745747 seconds, bootstrap likelihood -153268.570482, best rearrangement setting 13 Bootstrap[93]: Time 6.241404 seconds, bootstrap likelihood -153581.860435, best rearrangement setting 15 Bootstrap[94]: Time 5.637602 seconds, bootstrap likelihood -152931.688493, best rearrangement setting 5 Bootstrap[95]: Time 5.655824 seconds, bootstrap likelihood -153601.668215, best rearrangement setting 5 Bootstrap[96]: Time 6.048683 seconds, bootstrap likelihood -154286.699259, best rearrangement setting 13 Bootstrap[97]: Time 5.829737 seconds, bootstrap likelihood -152983.204239, best rearrangement setting 11 Bootstrap[98]: Time 6.050810 seconds, bootstrap likelihood -154237.140430, best rearrangement setting 6 Bootstrap[99]: Time 5.707582 seconds, bootstrap likelihood -153102.824639, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 676.087994 seconds Average Time per Rapid Bootstrap 6.760880 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 2016.909221 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 93.086281 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.628083 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.165135 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.011446 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 677.934395 seconds Printed linked AA GTR matrix that achieved an overall improvement of 2016.129074 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 93.071116 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 64.027330 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 551.953750 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 40.201352 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.382864 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.146531 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.024621 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2149.262220 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 113.338839 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 6.144852 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.369071 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.038234 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -162454.742514 Slow ML Search 1 Likelihood: -162454.742514 Slow ML Search 2 Likelihood: -162454.742514 Slow ML Search 3 Likelihood: -162454.742515 Slow ML Search 4 Likelihood: -162454.742513 Slow ML Search 5 Likelihood: -162454.742514 Slow ML Search 6 Likelihood: -162454.742514 Slow ML Search 7 Likelihood: -162454.742514 Slow ML Search 8 Likelihood: -162454.742514 Slow ML Search 9 Likelihood: -162454.742515 Slow ML optimization finished Slow ML search Time: 885.158033 seconds Printed linked AA GTR matrix that achieved an overall improvement of 2148.983398 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 113.325217 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 6.185468 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.379683 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.039690 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov_Partition_No Name Provided Thorough ML search Time: 497.360953 seconds Final ML Optimization Likelihood: -162454.728470 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.567186 Tree-Length: 7.822822 rate A <-> R: 0.414531 rate A <-> N: 0.524600 rate A <-> D: 3.047099 rate A <-> C: 4.571945 rate A <-> Q: 0.465374 rate A <-> E: 3.807092 rate A <-> G: 7.274363 rate A <-> H: 0.153339 rate A <-> I: 1.938973 rate A <-> L: 1.340254 rate A <-> K: 0.254682 rate A <-> M: 1.100355 rate A <-> F: 0.952398 rate A <-> P: 5.334661 rate A <-> S: 21.944362 rate A <-> T: 16.131555 rate A <-> W: 0.136673 rate A <-> Y: 0.022952 rate A <-> V: 14.840049 rate R <-> N: 0.148252 rate R <-> D: 0.087989 rate R <-> C: 1.215248 rate R <-> Q: 6.596665 rate R <-> E: 0.984734 rate R <-> G: 2.053713 rate R <-> H: 4.323613 rate R <-> I: 0.293092 rate R <-> L: 0.510930 rate R <-> K: 22.657992 rate R <-> M: 1.106795 rate R <-> F: 0.132416 rate R <-> P: 0.927067 rate R <-> S: 1.402180 rate R <-> T: 0.687294 rate R <-> W: 0.905529 rate R <-> Y: 0.280999 rate R <-> V: 0.000000 rate N <-> D: 14.595206 rate N <-> C: 1.102223 rate N <-> Q: 6.673980 rate N <-> E: 2.756194 rate N <-> G: 2.315784 rate N <-> H: 8.518805 rate N <-> I: 2.830305 rate N <-> L: 0.833211 rate N <-> K: 8.549053 rate N <-> M: 0.620040 rate N <-> F: 0.609594 rate N <-> P: 0.291276 rate N <-> S: 15.219572 rate N <-> T: 8.579177 rate N <-> W: 0.195499 rate N <-> Y: 3.576993 rate N <-> V: 0.357547 rate D <-> C: 0.704204 rate D <-> Q: 0.038932 rate D <-> E: 34.256214 rate D <-> G: 3.938822 rate D <-> H: 1.440460 rate D <-> I: 0.218043 rate D <-> L: 0.207801 rate D <-> K: 1.079606 rate D <-> M: 0.249964 rate D <-> F: 0.127529 rate D <-> P: 1.506026 rate D <-> S: 3.474338 rate D <-> T: 1.790895 rate D <-> W: 0.164753 rate D <-> Y: 0.719984 rate D <-> V: 0.447194 rate C <-> Q: 0.000000 rate C <-> E: 0.000000 rate C <-> G: 3.315482 rate C <-> H: 3.385805 rate C <-> I: 1.035027 rate C <-> L: 1.177560 rate C <-> K: 0.000000 rate C <-> M: 2.325904 rate C <-> F: 1.801095 rate C <-> P: 0.051346 rate C <-> S: 9.688375 rate C <-> T: 2.768083 rate C <-> W: 0.780570 rate C <-> Y: 5.304645 rate C <-> V: 4.110317 rate Q <-> E: 8.987124 rate Q <-> G: 0.000000 rate Q <-> H: 24.759617 rate Q <-> I: 0.586980 rate Q <-> L: 1.833926 rate Q <-> K: 7.372160 rate Q <-> M: 1.822315 rate Q <-> F: 0.347361 rate Q <-> P: 3.982831 rate Q <-> S: 2.463653 rate Q <-> T: 1.424022 rate Q <-> W: 0.000000 rate Q <-> Y: 1.947744 rate Q <-> V: 0.198699 rate E <-> G: 4.045842 rate E <-> H: 1.137956 rate E <-> I: 0.145499 rate E <-> L: 0.378713 rate E <-> K: 4.253330 rate E <-> M: 0.000000 rate E <-> F: 0.077011 rate E <-> P: 1.246003 rate E <-> S: 2.266580 rate E <-> T: 1.676971 rate E <-> W: 0.141938 rate E <-> Y: 0.622005 rate E <-> V: 1.220361 rate G <-> H: 0.681248 rate G <-> I: 0.132674 rate G <-> L: 0.055760 rate G <-> K: 0.327711 rate G <-> M: 0.089158 rate G <-> F: 0.273368 rate G <-> P: 0.133221 rate G <-> S: 6.752541 rate G <-> T: 0.526575 rate G <-> W: 0.936234 rate G <-> Y: 0.000000 rate G <-> V: 0.913249 rate H <-> I: 0.164901 rate H <-> L: 1.043726 rate H <-> K: 0.462377 rate H <-> M: 0.000000 rate H <-> F: 0.564021 rate H <-> P: 1.357953 rate H <-> S: 1.800180 rate H <-> T: 1.766031 rate H <-> W: 0.470292 rate H <-> Y: 14.474606 rate H <-> V: 0.000000 rate I <-> L: 16.721538 rate I <-> K: 1.539473 rate I <-> M: 16.748502 rate I <-> F: 3.301356 rate I <-> P: 0.013875 rate I <-> S: 1.128226 rate I <-> T: 9.062011 rate I <-> W: 0.385457 rate I <-> Y: 2.371921 rate I <-> V: 48.919886 rate L <-> K: 0.613082 rate L <-> M: 13.216176 rate L <-> F: 5.869341 rate L <-> P: 1.530109 rate L <-> S: 1.795980 rate L <-> T: 1.776771 rate L <-> W: 1.318579 rate L <-> Y: 1.274250 rate L <-> V: 4.504349 rate K <-> M: 0.619265 rate K <-> F: 0.132958 rate K <-> P: 0.573839 rate K <-> S: 1.951940 rate K <-> T: 1.815580 rate K <-> W: 0.182663 rate K <-> Y: 0.768635 rate K <-> V: 0.335327 rate M <-> F: 1.154651 rate M <-> P: 0.000000 rate M <-> S: 0.716042 rate M <-> T: 5.875225 rate M <-> W: 0.378593 rate M <-> Y: 1.006849 rate M <-> V: 8.076404 rate F <-> P: 0.240541 rate F <-> S: 1.335580 rate F <-> T: 0.654301 rate F <-> W: 0.986974 rate F <-> Y: 9.842208 rate F <-> V: 1.331611 rate P <-> S: 6.894776 rate P <-> T: 3.657164 rate P <-> W: 0.379624 rate P <-> Y: 1.013566 rate P <-> V: 1.481972 rate S <-> T: 21.368253 rate S <-> W: 0.368404 rate S <-> Y: 1.570032 rate S <-> V: 1.410208 rate T <-> W: 0.000000 rate T <-> Y: 0.862432 rate T <-> V: 11.961866 rate W <-> Y: 1.634380 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.042956 freq pi(R): 0.037171 freq pi(N): 0.064863 freq pi(D): 0.029496 freq pi(C): 0.012366 freq pi(Q): 0.017418 freq pi(E): 0.036624 freq pi(G): 0.039462 freq pi(H): 0.016618 freq pi(I): 0.074237 freq pi(L): 0.123781 freq pi(K): 0.081814 freq pi(M): 0.016969 freq pi(F): 0.142345 freq pi(P): 0.021619 freq pi(S): 0.074493 freq pi(T): 0.044572 freq pi(W): 0.015216 freq pi(Y): 0.053513 freq pi(V): 0.054467 ML search took 2060.544802 secs or 0.572374 hours Combined Bootstrap and ML search took 2736.636981 secs or 0.760177 hours Drawing Bootstrap Support Values on best-scoring ML tree ... Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bootstrap.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov Best-scoring ML tree written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov Best-scoring ML tree with support values written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitions.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov Best-scoring ML tree with support values as branch labels written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitionsBranchLabels.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.50perc_cov Overall execution time for full ML analysis: 2736.886820 secs or 0.760246 hours or 0.031677 days