IMPORTANT WARNING: Alignment column 1 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 2 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 3 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 4 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 5 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 6 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 8 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7177 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7178 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7179 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7180 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7181 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7182 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7183 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7184 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7185 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7186 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7187 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7188 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7189 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7190 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7191 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7192 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7193 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7194 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7195 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7196 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7197 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7198 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7945 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7946 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7947 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7948 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7949 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7950 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7951 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7952 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7953 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7954 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7955 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 7956 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14225 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14226 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14227 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14228 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 14229 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 16924 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 48 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 undetermined columns removed is printed to file supermatrix.mito.full-assemblies.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 12643 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 43.49% 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: 12643 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.fa -n RAxML-PROTCATGTR-supermatrix.mito.full-assemblies -m PROTCATGTR -T 16 -p 12345 -N 100 -x 12345 Printed linked AA GTR matrix that achieved an overall improvement of 12581.643517 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 9592.141706 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 461.329792 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 21.226102 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 1.881459 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_Partition_No Name Provided Time for BS model parameter optimization 255.325663 Bootstrap[0]: Time 268.489948 seconds, bootstrap likelihood -206999.677937, best rearrangement setting 13 Bootstrap[1]: Time 11.802572 seconds, bootstrap likelihood -206567.733076, best rearrangement setting 13 Bootstrap[2]: Time 11.966898 seconds, bootstrap likelihood -203284.515536, best rearrangement setting 12 Bootstrap[3]: Time 11.891105 seconds, bootstrap likelihood -205462.641758, best rearrangement setting 15 Bootstrap[4]: Time 12.369170 seconds, bootstrap likelihood -205320.607326, best rearrangement setting 10 Bootstrap[5]: Time 12.422980 seconds, bootstrap likelihood -205567.343295, best rearrangement setting 10 Bootstrap[6]: Time 12.000141 seconds, bootstrap likelihood -208437.551068, best rearrangement setting 6 Bootstrap[7]: Time 12.164462 seconds, bootstrap likelihood -206145.457354, best rearrangement setting 14 Bootstrap[8]: Time 11.018185 seconds, bootstrap likelihood -207294.492535, best rearrangement setting 5 Bootstrap[9]: Time 11.727275 seconds, bootstrap likelihood -208079.509698, best rearrangement setting 7 Bootstrap[10]: Time 12.460163 seconds, bootstrap likelihood -204796.749666, best rearrangement setting 7 Bootstrap[11]: Time 11.350908 seconds, bootstrap likelihood -206483.561036, best rearrangement setting 5 Bootstrap[12]: Time 12.440444 seconds, bootstrap likelihood -203488.504589, best rearrangement setting 8 Bootstrap[13]: Time 12.092420 seconds, bootstrap likelihood -205426.270406, best rearrangement setting 7 Bootstrap[14]: Time 12.375817 seconds, bootstrap likelihood -204467.475775, best rearrangement setting 12 Bootstrap[15]: Time 12.305853 seconds, bootstrap likelihood -206764.823621, best rearrangement setting 15 Bootstrap[16]: Time 4.015372 seconds, bootstrap likelihood -207431.728282, best rearrangement setting 12 Bootstrap[17]: Time 11.942752 seconds, bootstrap likelihood -205276.925897, best rearrangement setting 12 Bootstrap[18]: Time 11.068643 seconds, bootstrap likelihood -206879.722990, best rearrangement setting 5 Bootstrap[19]: Time 12.548131 seconds, bootstrap likelihood -204774.770396, best rearrangement setting 8 Bootstrap[20]: Time 12.467374 seconds, bootstrap likelihood -208577.770880, best rearrangement setting 10 Bootstrap[21]: Time 12.560457 seconds, bootstrap likelihood -207371.107362, best rearrangement setting 6 Bootstrap[22]: Time 10.636570 seconds, bootstrap likelihood -205515.323707, best rearrangement setting 5 Bootstrap[23]: Time 12.451910 seconds, bootstrap likelihood -202395.216851, best rearrangement setting 7 Bootstrap[24]: Time 3.976554 seconds, bootstrap likelihood -207391.170485, best rearrangement setting 8 Bootstrap[25]: Time 11.621991 seconds, bootstrap likelihood -206191.123473, best rearrangement setting 6 Bootstrap[26]: Time 12.002165 seconds, bootstrap likelihood -207020.314961, best rearrangement setting 12 Bootstrap[27]: Time 11.566549 seconds, bootstrap likelihood -205084.472131, best rearrangement setting 10 Bootstrap[28]: Time 12.578741 seconds, bootstrap likelihood -204414.771796, best rearrangement setting 11 Bootstrap[29]: Time 12.243921 seconds, bootstrap likelihood -204880.306397, best rearrangement setting 12 Bootstrap[30]: Time 4.358967 seconds, bootstrap likelihood -204474.663027, best rearrangement setting 15 Bootstrap[31]: Time 4.136274 seconds, bootstrap likelihood -207379.010472, best rearrangement setting 15 Bootstrap[32]: Time 11.492579 seconds, bootstrap likelihood -205320.658543, best rearrangement setting 6 Bootstrap[33]: Time 12.135364 seconds, bootstrap likelihood -204285.136459, best rearrangement setting 15 Bootstrap[34]: Time 12.354839 seconds, bootstrap likelihood -205471.203957, best rearrangement setting 11 Bootstrap[35]: Time 12.636186 seconds, bootstrap likelihood -205823.143479, best rearrangement setting 8 Bootstrap[36]: Time 12.011877 seconds, bootstrap likelihood -205846.437537, best rearrangement setting 9 Bootstrap[37]: Time 11.984903 seconds, bootstrap likelihood -207002.746532, best rearrangement setting 11 Bootstrap[38]: Time 11.914418 seconds, bootstrap likelihood -207997.482212, best rearrangement setting 8 Bootstrap[39]: Time 4.021289 seconds, bootstrap likelihood -208001.245888, best rearrangement setting 13 Bootstrap[40]: Time 12.574982 seconds, bootstrap likelihood -206521.374318, best rearrangement setting 13 Bootstrap[41]: Time 11.503654 seconds, bootstrap likelihood -204701.337616, best rearrangement setting 10 Bootstrap[42]: Time 4.064567 seconds, bootstrap likelihood -203281.888099, best rearrangement setting 5 Bootstrap[43]: Time 12.007098 seconds, bootstrap likelihood -205644.864583, best rearrangement setting 14 Bootstrap[44]: Time 11.774408 seconds, bootstrap likelihood -205532.172666, best rearrangement setting 10 Bootstrap[45]: Time 12.113201 seconds, bootstrap likelihood -205713.326799, best rearrangement setting 15 Bootstrap[46]: Time 12.309074 seconds, bootstrap likelihood -204346.896058, best rearrangement setting 14 Bootstrap[47]: Time 12.590873 seconds, bootstrap likelihood -206522.481658, best rearrangement setting 8 Bootstrap[48]: Time 11.815852 seconds, bootstrap likelihood -205912.566369, best rearrangement setting 6 Bootstrap[49]: Time 3.897315 seconds, bootstrap likelihood -206102.541276, best rearrangement setting 7 Bootstrap[50]: Time 12.740272 seconds, bootstrap likelihood -207114.810709, best rearrangement setting 7 Bootstrap[51]: Time 12.747030 seconds, bootstrap likelihood -204353.539935, best rearrangement setting 11 Bootstrap[52]: Time 12.267911 seconds, bootstrap likelihood -205795.601461, best rearrangement setting 12 Bootstrap[53]: Time 12.561799 seconds, bootstrap likelihood -206444.943617, best rearrangement setting 8 Bootstrap[54]: Time 12.441591 seconds, bootstrap likelihood -204991.427670, best rearrangement setting 9 Bootstrap[55]: Time 12.378315 seconds, bootstrap likelihood -205673.643548, best rearrangement setting 11 Bootstrap[56]: Time 11.429336 seconds, bootstrap likelihood -205686.977065, best rearrangement setting 5 Bootstrap[57]: Time 12.175411 seconds, bootstrap likelihood -206313.097961, best rearrangement setting 7 Bootstrap[58]: Time 12.310544 seconds, bootstrap likelihood -205429.282395, best rearrangement setting 10 Bootstrap[59]: Time 4.054924 seconds, bootstrap likelihood -204998.570276, best rearrangement setting 9 Bootstrap[60]: Time 12.392166 seconds, bootstrap likelihood -205689.747324, best rearrangement setting 7 Bootstrap[61]: Time 11.231180 seconds, bootstrap likelihood -206562.702870, best rearrangement setting 5 Bootstrap[62]: Time 12.709757 seconds, bootstrap likelihood -206238.766731, best rearrangement setting 11 Bootstrap[63]: Time 11.972412 seconds, bootstrap likelihood -207891.435293, best rearrangement setting 12 Bootstrap[64]: Time 12.609315 seconds, bootstrap likelihood -206467.546413, best rearrangement setting 7 Bootstrap[65]: Time 11.646143 seconds, bootstrap likelihood -208217.531338, best rearrangement setting 5 Bootstrap[66]: Time 11.030775 seconds, bootstrap likelihood -206693.684426, best rearrangement setting 5 Bootstrap[67]: Time 4.150461 seconds, bootstrap likelihood -204972.826641, best rearrangement setting 15 Bootstrap[68]: Time 12.193578 seconds, bootstrap likelihood -205996.486441, best rearrangement setting 11 Bootstrap[69]: Time 3.901072 seconds, bootstrap likelihood -205953.143041, best rearrangement setting 5 Bootstrap[70]: Time 12.304436 seconds, bootstrap likelihood -205232.643770, best rearrangement setting 8 Bootstrap[71]: Time 4.123608 seconds, bootstrap likelihood -204776.374771, best rearrangement setting 10 Bootstrap[72]: Time 12.279589 seconds, bootstrap likelihood -207387.071270, best rearrangement setting 11 Bootstrap[73]: Time 11.776629 seconds, bootstrap likelihood -207562.335060, best rearrangement setting 9 Bootstrap[74]: Time 11.216266 seconds, bootstrap likelihood -205436.738401, best rearrangement setting 5 Bootstrap[75]: Time 12.009748 seconds, bootstrap likelihood -206771.666772, best rearrangement setting 8 Bootstrap[76]: Time 12.320664 seconds, bootstrap likelihood -206556.605514, best rearrangement setting 9 Bootstrap[77]: Time 12.075261 seconds, bootstrap likelihood -207875.217397, best rearrangement setting 11 Bootstrap[78]: Time 12.025121 seconds, bootstrap likelihood -205268.060074, best rearrangement setting 15 Bootstrap[79]: Time 12.722241 seconds, bootstrap likelihood -205926.807511, best rearrangement setting 9 Bootstrap[80]: Time 4.614680 seconds, bootstrap likelihood -205186.730472, best rearrangement setting 15 Bootstrap[81]: Time 12.070894 seconds, bootstrap likelihood -204541.769812, best rearrangement setting 7 Bootstrap[82]: Time 3.972981 seconds, bootstrap likelihood -205749.682779, best rearrangement setting 6 Bootstrap[83]: Time 12.180086 seconds, bootstrap likelihood -207361.442621, best rearrangement setting 10 Bootstrap[84]: Time 12.669254 seconds, bootstrap likelihood -206726.001751, best rearrangement setting 11 Bootstrap[85]: Time 12.254548 seconds, bootstrap likelihood -206248.762677, best rearrangement setting 8 Bootstrap[86]: Time 12.331219 seconds, bootstrap likelihood -204907.014978, best rearrangement setting 7 Bootstrap[87]: Time 11.840474 seconds, bootstrap likelihood -205223.166005, best rearrangement setting 7 Bootstrap[88]: Time 4.017311 seconds, bootstrap likelihood -204458.321822, best rearrangement setting 12 Bootstrap[89]: Time 4.005015 seconds, bootstrap likelihood -207040.406867, best rearrangement setting 10 Bootstrap[90]: Time 4.271485 seconds, bootstrap likelihood -205618.332450, best rearrangement setting 8 Bootstrap[91]: Time 12.530604 seconds, bootstrap likelihood -205984.608446, best rearrangement setting 12 Bootstrap[92]: Time 4.030263 seconds, bootstrap likelihood -207332.176921, best rearrangement setting 13 Bootstrap[93]: Time 12.416589 seconds, bootstrap likelihood -208619.278457, best rearrangement setting 15 Bootstrap[94]: Time 11.501997 seconds, bootstrap likelihood -205294.092699, best rearrangement setting 5 Bootstrap[95]: Time 11.556791 seconds, bootstrap likelihood -206063.375775, best rearrangement setting 5 Bootstrap[96]: Time 12.267087 seconds, bootstrap likelihood -204967.869773, best rearrangement setting 13 Bootstrap[97]: Time 12.123686 seconds, bootstrap likelihood -208340.022110, best rearrangement setting 11 Bootstrap[98]: Time 11.788839 seconds, bootstrap likelihood -204459.444283, best rearrangement setting 6 Bootstrap[99]: Time 12.093331 seconds, bootstrap likelihood -205053.455582, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 1329.180051 seconds Average Time per Rapid Bootstrap 13.291801 seconds Starting ML Search ... Printed linked AA GTR matrix that achieved an overall improvement of 2222.712796 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 115.372751 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.203368 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.351168 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.027581 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_Partition_No Name Provided Fast ML optimization finished Fast ML search Time: 961.016742 seconds Printed linked AA GTR matrix that achieved an overall improvement of 2222.088112 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 115.402446 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 5.207031 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.351570 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.027598 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 2310.204157 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 164.293679 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 19.450634 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.502957 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.737304 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.165561 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.046125 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_Partition_No Name Provided Slow ML Search 0 Likelihood: -218573.762711 Slow ML Search 1 Likelihood: -218573.762711 Slow ML Search 2 Likelihood: -218573.762711 Slow ML Search 3 Likelihood: -218573.762712 Slow ML Search 4 Likelihood: -218573.762711 Slow ML Search 5 Likelihood: -218573.762712 Slow ML Search 6 Likelihood: -218573.762711 Slow ML Search 7 Likelihood: -218573.762711 Slow ML Search 8 Likelihood: -218573.762711 Slow ML Search 9 Likelihood: -218573.762711 Slow ML optimization finished Slow ML search Time: 1566.383900 seconds Printed linked AA GTR matrix that achieved an overall improvement of 2310.385236 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 164.055002 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 19.423691 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 3.507147 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.739665 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.166362 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_Partition_No Name Provided Printed linked AA GTR matrix that achieved an overall improvement of 0.046397 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_Partition_No Name Provided Thorough ML search Time: 1073.012299 seconds Final ML Optimization Likelihood: -218573.775428 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.615442 Tree-Length: 26.684954 rate A <-> R: 0.482977 rate A <-> N: 0.621103 rate A <-> D: 2.537414 rate A <-> C: 6.372924 rate A <-> Q: 1.082943 rate A <-> E: 3.770551 rate A <-> G: 7.777590 rate A <-> H: 0.445033 rate A <-> I: 1.819993 rate A <-> L: 1.535812 rate A <-> K: 0.270528 rate A <-> M: 1.558294 rate A <-> F: 0.822187 rate A <-> P: 4.783738 rate A <-> S: 20.933679 rate A <-> T: 15.115926 rate A <-> W: 0.058435 rate A <-> Y: 0.000000 rate A <-> V: 14.576026 rate R <-> N: 0.407153 rate R <-> D: 0.229375 rate R <-> C: 1.799965 rate R <-> Q: 5.672823 rate R <-> E: 0.778038 rate R <-> G: 1.881796 rate R <-> H: 5.368239 rate R <-> I: 0.323367 rate R <-> L: 0.473113 rate R <-> K: 19.775903 rate R <-> M: 1.333919 rate R <-> F: 0.088208 rate R <-> P: 1.164467 rate R <-> S: 1.432476 rate R <-> T: 0.929745 rate R <-> W: 1.445356 rate R <-> Y: 0.467423 rate R <-> V: 0.306072 rate N <-> D: 15.621096 rate N <-> C: 0.960379 rate N <-> Q: 6.617697 rate N <-> E: 2.919504 rate N <-> G: 2.153609 rate N <-> H: 8.345841 rate N <-> I: 2.830885 rate N <-> L: 0.794995 rate N <-> K: 8.294526 rate N <-> M: 0.773395 rate N <-> F: 0.647188 rate N <-> P: 0.356166 rate N <-> S: 14.838137 rate N <-> T: 8.557127 rate N <-> W: 0.115364 rate N <-> Y: 3.383297 rate N <-> V: 0.415196 rate D <-> C: 0.677385 rate D <-> Q: 0.000000 rate D <-> E: 35.459732 rate D <-> G: 3.853820 rate D <-> H: 2.279371 rate D <-> I: 0.296297 rate D <-> L: 0.357603 rate D <-> K: 1.190745 rate D <-> M: 0.051737 rate D <-> F: 0.099046 rate D <-> P: 1.674737 rate D <-> S: 4.199416 rate D <-> T: 2.652130 rate D <-> W: 0.161398 rate D <-> Y: 0.577477 rate D <-> V: 0.751132 rate C <-> Q: 0.129928 rate C <-> E: 0.000000 rate C <-> G: 3.277019 rate C <-> H: 3.628370 rate C <-> I: 1.168720 rate C <-> L: 1.592418 rate C <-> K: 0.000000 rate C <-> M: 1.703005 rate C <-> F: 1.848354 rate C <-> P: 0.029867 rate C <-> S: 9.425928 rate C <-> T: 3.208033 rate C <-> W: 1.290401 rate C <-> Y: 5.353153 rate C <-> V: 4.569445 rate Q <-> E: 8.338917 rate Q <-> G: 0.286374 rate Q <-> H: 24.269057 rate Q <-> I: 0.400445 rate Q <-> L: 1.894494 rate Q <-> K: 7.207135 rate Q <-> M: 1.877168 rate Q <-> F: 0.356993 rate Q <-> P: 4.328227 rate Q <-> S: 2.621530 rate Q <-> T: 2.806667 rate Q <-> W: 0.000000 rate Q <-> Y: 1.968090 rate Q <-> V: 0.581468 rate E <-> G: 3.892995 rate E <-> H: 1.180570 rate E <-> I: 0.395311 rate E <-> L: 0.592741 rate E <-> K: 4.396945 rate E <-> M: 0.237811 rate E <-> F: 0.132863 rate E <-> P: 1.486494 rate E <-> S: 2.771170 rate E <-> T: 3.157466 rate E <-> W: 0.186673 rate E <-> Y: 0.642467 rate E <-> V: 1.127715 rate G <-> H: 0.495208 rate G <-> I: 0.135119 rate G <-> L: 0.070122 rate G <-> K: 0.381097 rate G <-> M: 0.359244 rate G <-> F: 0.221344 rate G <-> P: 0.475160 rate G <-> S: 6.306917 rate G <-> T: 0.492863 rate G <-> W: 1.128404 rate G <-> Y: 0.049829 rate G <-> V: 0.946238 rate H <-> I: 0.201117 rate H <-> L: 1.017982 rate H <-> K: 0.374591 rate H <-> M: 0.000000 rate H <-> F: 0.546493 rate H <-> P: 2.098732 rate H <-> S: 2.096408 rate H <-> T: 1.607130 rate H <-> W: 0.649895 rate H <-> Y: 13.905994 rate H <-> V: 0.000000 rate I <-> L: 16.739120 rate I <-> K: 1.664799 rate I <-> M: 15.192271 rate I <-> F: 3.317482 rate I <-> P: 0.095217 rate I <-> S: 1.142568 rate I <-> T: 8.827726 rate I <-> W: 0.325800 rate I <-> Y: 2.513720 rate I <-> V: 45.829870 rate L <-> K: 0.665034 rate L <-> M: 13.373489 rate L <-> F: 5.805173 rate L <-> P: 1.818776 rate L <-> S: 1.969644 rate L <-> T: 1.931179 rate L <-> W: 1.434993 rate L <-> Y: 1.358546 rate L <-> V: 4.452310 rate K <-> M: 0.650202 rate K <-> F: 0.139309 rate K <-> P: 0.549598 rate K <-> S: 1.905689 rate K <-> T: 1.841356 rate K <-> W: 0.136200 rate K <-> Y: 0.733376 rate K <-> V: 0.344667 rate M <-> F: 1.346636 rate M <-> P: 0.005607 rate M <-> S: 0.561367 rate M <-> T: 5.279860 rate M <-> W: 0.358977 rate M <-> Y: 0.921443 rate M <-> V: 8.862052 rate F <-> P: 0.356241 rate F <-> S: 1.459422 rate F <-> T: 0.697488 rate F <-> W: 1.189791 rate F <-> Y: 9.623887 rate F <-> V: 1.353829 rate P <-> S: 7.240390 rate P <-> T: 3.497271 rate P <-> W: 0.590491 rate P <-> Y: 0.970029 rate P <-> V: 1.888779 rate S <-> T: 21.534063 rate S <-> W: 0.614181 rate S <-> Y: 1.605622 rate S <-> V: 1.530735 rate T <-> W: 0.409759 rate T <-> Y: 1.018803 rate T <-> V: 11.441830 rate W <-> Y: 2.556294 rate W <-> V: 0.159701 rate Y <-> V: 1.000000 freq pi(A): 0.042203 freq pi(R): 0.037092 freq pi(N): 0.066377 freq pi(D): 0.030762 freq pi(C): 0.012280 freq pi(Q): 0.017756 freq pi(E): 0.037922 freq pi(G): 0.039108 freq pi(H): 0.016507 freq pi(I): 0.074642 freq pi(L): 0.123443 freq pi(K): 0.081772 freq pi(M): 0.017046 freq pi(F): 0.138925 freq pi(P): 0.022072 freq pi(S): 0.075230 freq pi(T): 0.044883 freq pi(W): 0.015220 freq pi(Y): 0.053208 freq pi(V): 0.053554 ML search took 3600.502793 secs or 1.000140 hours Combined Bootstrap and ML search took 4929.683650 secs or 1.369357 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 Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bootstrap.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies Best-scoring ML tree written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTCATGTR-supermatrix.mito.full-assemblies 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 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 Overall execution time for full ML analysis: 4929.737906 secs or 1.369372 hours or 0.057057 days