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 7781 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 13.57% 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: 7781 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.80perc_cov.fa -n RAxML-PROTCATGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.80perc_cov -m PROTCATGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 13561.001834 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1956.067558 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 91.737690 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.821607 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.80perc_cov_Partition_No Name Provided Time for BS model parameter optimization 117.703395 Bootstrap[0]: Time 123.532761 seconds, bootstrap likelihood -137991.963660, best rearrangement setting 13 Bootstrap[1]: Time 5.252643 seconds, bootstrap likelihood -137544.915090, best rearrangement setting 13 Bootstrap[2]: Time 5.421519 seconds, bootstrap likelihood -139627.792237, best rearrangement setting 12 Bootstrap[3]: Time 5.017461 seconds, bootstrap likelihood -140250.868598, best rearrangement setting 15 Bootstrap[4]: Time 5.293707 seconds, bootstrap likelihood -139389.913104, best rearrangement setting 10 Bootstrap[5]: Time 5.378974 seconds, bootstrap likelihood -139496.440190, best rearrangement setting 10 Bootstrap[6]: Time 5.526165 seconds, bootstrap likelihood -139735.279182, best rearrangement setting 6 Bootstrap[7]: Time 5.488305 seconds, bootstrap likelihood -140591.677857, best rearrangement setting 14 Bootstrap[8]: Time 5.317978 seconds, bootstrap likelihood -137365.794100, best rearrangement setting 5 Bootstrap[9]: Time 2.126988 seconds, bootstrap likelihood -139115.285950, best rearrangement setting 7 Bootstrap[10]: Time 5.881786 seconds, bootstrap likelihood -140494.131246, best rearrangement setting 7 Bootstrap[11]: Time 5.539118 seconds, bootstrap likelihood -140716.807184, best rearrangement setting 5 Bootstrap[12]: Time 2.153919 seconds, bootstrap likelihood -138565.069189, best rearrangement setting 8 Bootstrap[13]: Time 5.402596 seconds, bootstrap likelihood -139510.093045, best rearrangement setting 7 Bootstrap[14]: Time 5.420539 seconds, bootstrap likelihood -138481.766765, best rearrangement setting 12 Bootstrap[15]: Time 5.349499 seconds, bootstrap likelihood -139733.803411, best rearrangement setting 15 Bootstrap[16]: Time 5.332578 seconds, bootstrap likelihood -139601.912406, best rearrangement setting 12 Bootstrap[17]: Time 5.498279 seconds, bootstrap likelihood -139811.446840, best rearrangement setting 12 Bootstrap[18]: Time 5.353051 seconds, bootstrap likelihood -139890.412291, best rearrangement setting 5 Bootstrap[19]: Time 5.669804 seconds, bootstrap likelihood -139954.171202, best rearrangement setting 8 Bootstrap[20]: Time 5.522927 seconds, bootstrap likelihood -138594.750796, best rearrangement setting 10 Bootstrap[21]: Time 5.078098 seconds, bootstrap likelihood -140065.260136, best rearrangement setting 6 Bootstrap[22]: Time 5.195838 seconds, bootstrap likelihood -138749.135586, best rearrangement setting 5 Bootstrap[23]: Time 5.297045 seconds, bootstrap likelihood -138702.891960, best rearrangement setting 7 Bootstrap[24]: Time 5.337846 seconds, bootstrap likelihood -139159.442358, best rearrangement setting 8 Bootstrap[25]: Time 5.355659 seconds, bootstrap likelihood -140221.977526, best rearrangement setting 6 Bootstrap[26]: Time 5.385740 seconds, bootstrap likelihood -137480.899547, best rearrangement setting 12 Bootstrap[27]: Time 5.455297 seconds, bootstrap likelihood -138805.042996, best rearrangement setting 10 Bootstrap[28]: Time 2.224578 seconds, bootstrap likelihood -138557.650135, best rearrangement setting 11 Bootstrap[29]: Time 5.323866 seconds, bootstrap likelihood -140181.046760, best rearrangement setting 12 Bootstrap[30]: Time 5.386319 seconds, bootstrap likelihood -138870.185301, best rearrangement setting 15 Bootstrap[31]: Time 5.519793 seconds, bootstrap likelihood -140253.533789, best rearrangement setting 15 Bootstrap[32]: Time 5.481213 seconds, bootstrap likelihood -139163.443020, best rearrangement setting 6 Bootstrap[33]: Time 5.288906 seconds, bootstrap likelihood -138631.597050, best rearrangement setting 15 Bootstrap[34]: Time 5.322249 seconds, bootstrap likelihood -139891.921127, best rearrangement setting 11 Bootstrap[35]: Time 5.492031 seconds, bootstrap likelihood -138290.663296, best rearrangement setting 8 Bootstrap[36]: Time 5.146753 seconds, bootstrap likelihood -139658.416695, best rearrangement setting 9 Bootstrap[37]: Time 5.349252 seconds, bootstrap likelihood -138474.085117, best rearrangement setting 11 Bootstrap[38]: Time 5.504113 seconds, bootstrap likelihood -140252.130230, best rearrangement setting 8 Bootstrap[39]: Time 5.343477 seconds, bootstrap likelihood -137205.949201, best rearrangement setting 13 Bootstrap[40]: Time 2.332307 seconds, bootstrap likelihood -139298.543033, best rearrangement setting 13 Bootstrap[41]: Time 2.339263 seconds, bootstrap likelihood -140208.097192, best rearrangement setting 10 Bootstrap[42]: Time 5.358506 seconds, bootstrap likelihood -140174.590425, best rearrangement setting 5 Bootstrap[43]: Time 5.334898 seconds, bootstrap likelihood -139215.427089, best rearrangement setting 14 Bootstrap[44]: Time 5.253384 seconds, bootstrap likelihood -136856.471179, best rearrangement setting 10 Bootstrap[45]: Time 5.352148 seconds, bootstrap likelihood -140154.368714, best rearrangement setting 15 Bootstrap[46]: Time 5.354374 seconds, bootstrap likelihood -140102.123281, best rearrangement setting 14 Bootstrap[47]: Time 5.407030 seconds, bootstrap likelihood -138315.024202, best rearrangement setting 8 Bootstrap[48]: Time 5.420503 seconds, bootstrap likelihood -137855.837156, best rearrangement setting 6 Bootstrap[49]: Time 5.453122 seconds, bootstrap likelihood -139351.306377, best rearrangement setting 7 Bootstrap[50]: Time 5.798633 seconds, bootstrap likelihood -139478.746166, best rearrangement setting 7 Bootstrap[51]: Time 5.306872 seconds, bootstrap likelihood -139447.913902, best rearrangement setting 11 Bootstrap[52]: Time 5.229288 seconds, bootstrap likelihood -137580.787287, best rearrangement setting 12 Bootstrap[53]: Time 5.410753 seconds, bootstrap likelihood -139011.760519, best rearrangement setting 8 Bootstrap[54]: Time 5.502439 seconds, bootstrap likelihood -139147.814967, best rearrangement setting 9 Bootstrap[55]: Time 5.500239 seconds, bootstrap likelihood -140124.753306, best rearrangement setting 11 Bootstrap[56]: Time 5.413797 seconds, bootstrap likelihood -140703.306797, best rearrangement setting 5 Bootstrap[57]: Time 5.585844 seconds, bootstrap likelihood -138385.384952, best rearrangement setting 7 Bootstrap[58]: Time 5.467665 seconds, bootstrap likelihood -137464.507924, best rearrangement setting 10 Bootstrap[59]: Time 5.479135 seconds, bootstrap likelihood -139375.484772, best rearrangement setting 9 Bootstrap[60]: Time 2.389833 seconds, bootstrap likelihood -140631.120700, best rearrangement setting 7 Bootstrap[61]: Time 5.374807 seconds, bootstrap likelihood -139247.265731, best rearrangement setting 5 Bootstrap[62]: Time 5.368273 seconds, bootstrap likelihood -139420.396964, best rearrangement setting 11 Bootstrap[63]: Time 5.517187 seconds, bootstrap likelihood -141300.764341, best rearrangement setting 12 Bootstrap[64]: Time 5.456403 seconds, bootstrap likelihood -140210.665011, best rearrangement setting 7 Bootstrap[65]: Time 5.357052 seconds, bootstrap likelihood -137466.872637, best rearrangement setting 5 Bootstrap[66]: Time 5.324621 seconds, bootstrap likelihood -138358.724006, best rearrangement setting 5 Bootstrap[67]: Time 5.408033 seconds, bootstrap likelihood -138476.894934, best rearrangement setting 15 Bootstrap[68]: Time 5.553601 seconds, bootstrap likelihood -139294.253083, best rearrangement setting 11 Bootstrap[69]: Time 5.254471 seconds, bootstrap likelihood -139253.221206, best rearrangement setting 5 Bootstrap[70]: Time 2.446423 seconds, bootstrap likelihood -137700.253751, best rearrangement setting 8 Bootstrap[71]: Time 5.607767 seconds, bootstrap likelihood -138362.891285, best rearrangement setting 10 Bootstrap[72]: Time 2.321079 seconds, bootstrap likelihood -139399.205661, best rearrangement setting 11 Bootstrap[73]: Time 5.690644 seconds, bootstrap likelihood -139154.705388, best rearrangement setting 9 Bootstrap[74]: Time 5.506512 seconds, bootstrap likelihood -139446.205299, best rearrangement setting 5 Bootstrap[75]: Time 5.217777 seconds, bootstrap likelihood -139431.256340, best rearrangement setting 8 Bootstrap[76]: Time 5.360444 seconds, bootstrap likelihood -138183.626806, best rearrangement setting 9 Bootstrap[77]: Time 5.191603 seconds, bootstrap likelihood -139370.009693, best rearrangement setting 11 Bootstrap[78]: Time 5.466685 seconds, bootstrap likelihood -138897.091873, best rearrangement setting 15 Bootstrap[79]: Time 5.550534 seconds, bootstrap likelihood -138725.649975, best rearrangement setting 9 Bootstrap[80]: Time 5.597244 seconds, bootstrap likelihood -138958.134797, best rearrangement setting 15 Bootstrap[81]: Time 5.297636 seconds, bootstrap likelihood -138566.113505, best rearrangement setting 7 Bootstrap[82]: Time 5.206518 seconds, bootstrap likelihood -138360.265677, best rearrangement setting 6 Bootstrap[83]: Time 5.435262 seconds, bootstrap likelihood -137998.989262, best rearrangement setting 10 Bootstrap[84]: Time 5.536281 seconds, bootstrap likelihood -139595.275256, best rearrangement setting 11 Bootstrap[85]: Time 5.612845 seconds, bootstrap likelihood -138167.776380, best rearrangement setting 8 Bootstrap[86]: Time 2.099903 seconds, bootstrap likelihood -138171.326792, best rearrangement setting 7 Bootstrap[87]: Time 5.497978 seconds, bootstrap likelihood -139279.602792, best rearrangement setting 7 Bootstrap[88]: Time 5.307084 seconds, bootstrap likelihood -138719.664091, best rearrangement setting 12 Bootstrap[89]: Time 5.308839 seconds, bootstrap likelihood -139353.344947, best rearrangement setting 10 Bootstrap[90]: Time 2.443839 seconds, bootstrap likelihood -139767.670759, best rearrangement setting 8 Bootstrap[91]: Time 5.360158 seconds, bootstrap likelihood -140676.454694, best rearrangement setting 12 Bootstrap[92]: Time 5.575098 seconds, bootstrap likelihood -138784.453154, best rearrangement setting 13 Bootstrap[93]: Time 5.396922 seconds, bootstrap likelihood -138439.204462, best rearrangement setting 15 Bootstrap[94]: Time 5.557901 seconds, bootstrap likelihood -137717.203440, best rearrangement setting 5 Bootstrap[95]: Time 5.286747 seconds, bootstrap likelihood -139277.441703, best rearrangement setting 5 Bootstrap[96]: Time 5.378664 seconds, bootstrap likelihood -140239.667111, best rearrangement setting 13 Bootstrap[97]: Time 2.162787 seconds, bootstrap likelihood -139272.901497, best rearrangement setting 11 Bootstrap[98]: Time 2.325799 seconds, bootstrap likelihood -140044.574674, best rearrangement setting 6 Bootstrap[99]: Time 5.527490 seconds, bootstrap likelihood -138608.060035, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 621.992652 seconds Average Time per Rapid Bootstrap 6.219927 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 2606.258774 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 439.271726 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 23.752983 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.776090 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.075446 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.80perc_cov_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 551.189814 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1792.609219 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 71.872486 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2.694841 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.126668 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.012874 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1942.554293 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 89.289478 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.023089 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.214382 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.025357 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.80perc_cov_Partition_No Name Provided Slow ML Search 0 Likelihood: -147601.605694 Slow ML Search 1 Likelihood: -147601.605695 Slow ML Search 2 Likelihood: -147601.605694 Slow ML Search 3 Likelihood: -147601.605695 Slow ML Search 4 Likelihood: -147601.605696 Slow ML Search 5 Likelihood: -147601.605695 Slow ML Search 6 Likelihood: -147601.605695 Slow ML Search 7 Likelihood: -147601.605695 Slow ML Search 8 Likelihood: -147601.605694 Slow ML Search 9 Likelihood: -147601.605695 Slow ML optimization finished Slow ML search Time: 718.083524 seconds Printed linked AA GTR matrix that achieved an overall improvement of 1942.730093 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 89.599430 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 4.038743 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.213206 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.80perc_cov_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.024930 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.80perc_cov_Partition_No Name Provided Thorough ML search Time: 447.190507 seconds Final ML Optimization Likelihood: -147601.598415 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.602313 Tree-Length: 6.608372 rate A <-> R: 0.332253 rate A <-> N: 0.529353 rate A <-> D: 2.966595 rate A <-> C: 4.768991 rate A <-> Q: 0.266938 rate A <-> E: 2.976449 rate A <-> G: 6.116165 rate A <-> H: 0.203197 rate A <-> I: 1.809009 rate A <-> L: 1.228776 rate A <-> K: 0.247388 rate A <-> M: 1.340083 rate A <-> F: 1.043476 rate A <-> P: 4.489987 rate A <-> S: 22.851084 rate A <-> T: 15.771889 rate A <-> W: 0.183376 rate A <-> Y: 0.072571 rate A <-> V: 14.714213 rate R <-> N: 0.169007 rate R <-> D: 0.000000 rate R <-> C: 0.977260 rate R <-> Q: 5.917459 rate R <-> E: 0.893971 rate R <-> G: 1.298207 rate R <-> H: 3.555735 rate R <-> I: 0.205614 rate R <-> L: 0.487700 rate R <-> K: 22.252283 rate R <-> M: 0.836790 rate R <-> F: 0.140191 rate R <-> P: 0.187168 rate R <-> S: 1.304825 rate R <-> T: 0.614294 rate R <-> W: 0.759966 rate R <-> Y: 0.270533 rate R <-> V: 0.000000 rate N <-> D: 14.496535 rate N <-> C: 1.066905 rate N <-> Q: 7.069668 rate N <-> E: 3.289265 rate N <-> G: 2.371374 rate N <-> H: 8.424657 rate N <-> I: 2.592170 rate N <-> L: 0.915962 rate N <-> K: 8.528647 rate N <-> M: 0.688933 rate N <-> F: 0.584507 rate N <-> P: 0.404799 rate N <-> S: 15.169007 rate N <-> T: 8.820294 rate N <-> W: 0.249699 rate N <-> Y: 3.719108 rate N <-> V: 0.257891 rate D <-> C: 0.903288 rate D <-> Q: 0.000000 rate D <-> E: 32.357518 rate D <-> G: 2.771904 rate D <-> H: 1.752532 rate D <-> I: 0.110634 rate D <-> L: 0.219302 rate D <-> K: 1.122097 rate D <-> M: 0.000000 rate D <-> F: 0.078669 rate D <-> P: 0.720259 rate D <-> S: 3.599664 rate D <-> T: 1.527980 rate D <-> W: 0.208005 rate D <-> Y: 0.583894 rate D <-> V: 0.300490 rate C <-> Q: 0.000000 rate C <-> E: 0.018160 rate C <-> G: 3.364003 rate C <-> H: 3.321733 rate C <-> I: 1.053731 rate C <-> L: 1.339701 rate C <-> K: 0.000000 rate C <-> M: 2.526989 rate C <-> F: 1.700171 rate C <-> P: 0.000000 rate C <-> S: 10.170959 rate C <-> T: 2.742486 rate C <-> W: 0.838471 rate C <-> Y: 5.120582 rate C <-> V: 4.408350 rate Q <-> E: 8.632092 rate Q <-> G: 0.000000 rate Q <-> H: 23.195544 rate Q <-> I: 0.616655 rate Q <-> L: 1.644257 rate Q <-> K: 7.255042 rate Q <-> M: 2.034108 rate Q <-> F: 0.282146 rate Q <-> P: 3.162239 rate Q <-> S: 2.099058 rate Q <-> T: 1.569111 rate Q <-> W: 0.000000 rate Q <-> Y: 1.708488 rate Q <-> V: 0.000000 rate E <-> G: 3.356874 rate E <-> H: 0.727290 rate E <-> I: 0.209605 rate E <-> L: 0.433314 rate E <-> K: 4.030236 rate E <-> M: 0.000000 rate E <-> F: 0.095751 rate E <-> P: 0.901886 rate E <-> S: 2.418827 rate E <-> T: 1.824069 rate E <-> W: 0.188846 rate E <-> Y: 0.661423 rate E <-> V: 1.016150 rate G <-> H: 0.677994 rate G <-> I: 0.133291 rate G <-> L: 0.042090 rate G <-> K: 0.291666 rate G <-> M: 0.123562 rate G <-> F: 0.295655 rate G <-> P: 0.125353 rate G <-> S: 6.749125 rate G <-> T: 0.596319 rate G <-> W: 0.677407 rate G <-> Y: 0.000000 rate G <-> V: 0.753499 rate H <-> I: 0.345689 rate H <-> L: 0.723619 rate H <-> K: 0.378308 rate H <-> M: 0.000000 rate H <-> F: 0.647618 rate H <-> P: 1.009379 rate H <-> S: 1.693490 rate H <-> T: 1.557160 rate H <-> W: 0.000000 rate H <-> Y: 13.065521 rate H <-> V: 0.000000 rate I <-> L: 17.367298 rate I <-> K: 1.353399 rate I <-> M: 16.514829 rate I <-> F: 3.316990 rate I <-> P: 0.059061 rate I <-> S: 1.184805 rate I <-> T: 8.960742 rate I <-> W: 0.446303 rate I <-> Y: 2.331052 rate I <-> V: 49.635407 rate L <-> K: 0.594023 rate L <-> M: 13.149471 rate L <-> F: 6.095024 rate L <-> P: 1.122604 rate L <-> S: 1.722422 rate L <-> T: 1.787001 rate L <-> W: 1.234456 rate L <-> Y: 1.288647 rate L <-> V: 4.842733 rate K <-> M: 0.599540 rate K <-> F: 0.123255 rate K <-> P: 0.356800 rate K <-> S: 2.035686 rate K <-> T: 1.903939 rate K <-> W: 0.187743 rate K <-> Y: 0.785078 rate K <-> V: 0.303870 rate M <-> F: 1.255465 rate M <-> P: 0.093076 rate M <-> S: 0.634161 rate M <-> T: 5.958022 rate M <-> W: 0.408331 rate M <-> Y: 0.736963 rate M <-> V: 7.302470 rate F <-> P: 0.183623 rate F <-> S: 1.327177 rate F <-> T: 0.608452 rate F <-> W: 1.016634 rate F <-> Y: 10.276345 rate F <-> V: 1.353806 rate P <-> S: 6.169821 rate P <-> T: 3.484029 rate P <-> W: 0.440591 rate P <-> Y: 0.939421 rate P <-> V: 1.270945 rate S <-> T: 21.806560 rate S <-> W: 0.208654 rate S <-> Y: 1.544489 rate S <-> V: 1.390942 rate T <-> W: 0.000000 rate T <-> Y: 0.939730 rate T <-> V: 11.914601 rate W <-> Y: 1.708759 rate W <-> V: 0.000000 rate Y <-> V: 1.000000 freq pi(A): 0.042462 freq pi(R): 0.036857 freq pi(N): 0.065339 freq pi(D): 0.028082 freq pi(C): 0.012491 freq pi(Q): 0.017258 freq pi(E): 0.034783 freq pi(G): 0.039187 freq pi(H): 0.016839 freq pi(I): 0.075018 freq pi(L): 0.123558 freq pi(K): 0.082078 freq pi(M): 0.017352 freq pi(F): 0.143328 freq pi(P): 0.021131 freq pi(S): 0.074342 freq pi(T): 0.044868 freq pi(W): 0.015216 freq pi(Y): 0.054578 freq pi(V): 0.055235 ML search took 1716.557380 secs or 0.476821 hours Combined Bootstrap and ML search took 2338.554836 secs or 0.649599 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.80perc_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.80perc_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.80perc_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.80perc_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.80perc_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.80perc_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.80perc_cov Overall execution time for full ML analysis: 2338.609118 secs or 0.649614 hours or 0.027067 days