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 6301 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 13.11%

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: 6301
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.95perc_cov.fa -n RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 



Printed linked AA GTR matrix that achieved an overall improvement of 1570.484800 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 67.362787 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 3.040154 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Time for BS model parameter optimization 174.907081
Bootstrap[0]: Time 190.396930 seconds, bootstrap likelihood -116358.008198, best rearrangement setting 13
Bootstrap[1]: Time 15.228668 seconds, bootstrap likelihood -116144.052189, best rearrangement setting 13
Bootstrap[2]: Time 6.607689 seconds, bootstrap likelihood -116494.035770, best rearrangement setting 12
Bootstrap[3]: Time 13.346789 seconds, bootstrap likelihood -115240.021029, best rearrangement setting 15
Bootstrap[4]: Time 14.086286 seconds, bootstrap likelihood -117484.338389, best rearrangement setting 10
Bootstrap[5]: Time 5.798963 seconds, bootstrap likelihood -116295.297982, best rearrangement setting 10
Bootstrap[6]: Time 14.184906 seconds, bootstrap likelihood -115877.446860, best rearrangement setting 6
Bootstrap[7]: Time 15.522161 seconds, bootstrap likelihood -117439.548600, best rearrangement setting 14
Bootstrap[8]: Time 14.531255 seconds, bootstrap likelihood -117467.062988, best rearrangement setting 5
Bootstrap[9]: Time 15.200528 seconds, bootstrap likelihood -115333.332973, best rearrangement setting 7
Bootstrap[10]: Time 14.981942 seconds, bootstrap likelihood -117315.782022, best rearrangement setting 7
Bootstrap[11]: Time 14.226974 seconds, bootstrap likelihood -115728.913515, best rearrangement setting 5
Bootstrap[12]: Time 16.131029 seconds, bootstrap likelihood -115817.073204, best rearrangement setting 8
Bootstrap[13]: Time 15.133571 seconds, bootstrap likelihood -116202.271211, best rearrangement setting 7
Bootstrap[14]: Time 15.861788 seconds, bootstrap likelihood -116705.805615, best rearrangement setting 12
Bootstrap[15]: Time 15.502294 seconds, bootstrap likelihood -117459.231409, best rearrangement setting 15
Bootstrap[16]: Time 6.623872 seconds, bootstrap likelihood -115832.932899, best rearrangement setting 12
Bootstrap[17]: Time 6.931934 seconds, bootstrap likelihood -116721.380108, best rearrangement setting 12
Bootstrap[18]: Time 14.731185 seconds, bootstrap likelihood -115825.569108, best rearrangement setting 5
Bootstrap[19]: Time 15.767322 seconds, bootstrap likelihood -116762.492572, best rearrangement setting 8
Bootstrap[20]: Time 16.044306 seconds, bootstrap likelihood -115651.027126, best rearrangement setting 10
Bootstrap[21]: Time 6.771857 seconds, bootstrap likelihood -116374.631567, best rearrangement setting 6
Bootstrap[22]: Time 15.372650 seconds, bootstrap likelihood -114979.780145, best rearrangement setting 5
Bootstrap[23]: Time 16.281967 seconds, bootstrap likelihood -116421.101205, best rearrangement setting 7
Bootstrap[24]: Time 15.835587 seconds, bootstrap likelihood -116567.752474, best rearrangement setting 8
Bootstrap[25]: Time 15.560363 seconds, bootstrap likelihood -116206.656973, best rearrangement setting 6
Bootstrap[26]: Time 15.177689 seconds, bootstrap likelihood -116188.596328, best rearrangement setting 12
Bootstrap[27]: Time 13.950157 seconds, bootstrap likelihood -114534.736039, best rearrangement setting 10
Bootstrap[28]: Time 15.972013 seconds, bootstrap likelihood -116800.776459, best rearrangement setting 11
Bootstrap[29]: Time 14.904163 seconds, bootstrap likelihood -115432.457968, best rearrangement setting 12
Bootstrap[30]: Time 15.959328 seconds, bootstrap likelihood -115924.158035, best rearrangement setting 15
Bootstrap[31]: Time 15.833993 seconds, bootstrap likelihood -117058.667628, best rearrangement setting 15
Bootstrap[32]: Time 15.443679 seconds, bootstrap likelihood -117230.568051, best rearrangement setting 6
Bootstrap[33]: Time 15.066408 seconds, bootstrap likelihood -117407.875151, best rearrangement setting 15
Bootstrap[34]: Time 15.877372 seconds, bootstrap likelihood -117378.971918, best rearrangement setting 11
Bootstrap[35]: Time 15.468020 seconds, bootstrap likelihood -115626.904963, best rearrangement setting 8
Bootstrap[36]: Time 15.961083 seconds, bootstrap likelihood -117046.996782, best rearrangement setting 9
Bootstrap[37]: Time 5.911830 seconds, bootstrap likelihood -116145.526382, best rearrangement setting 11
Bootstrap[38]: Time 6.424198 seconds, bootstrap likelihood -116534.106687, best rearrangement setting 8
Bootstrap[39]: Time 15.757683 seconds, bootstrap likelihood -114977.586868, best rearrangement setting 13
Bootstrap[40]: Time 6.710055 seconds, bootstrap likelihood -117625.860330, best rearrangement setting 13
Bootstrap[41]: Time 6.316607 seconds, bootstrap likelihood -117204.987511, best rearrangement setting 10
Bootstrap[42]: Time 6.608827 seconds, bootstrap likelihood -116943.779585, best rearrangement setting 5
Bootstrap[43]: Time 6.341970 seconds, bootstrap likelihood -115275.864698, best rearrangement setting 14
Bootstrap[44]: Time 6.616185 seconds, bootstrap likelihood -116513.985277, best rearrangement setting 10
Bootstrap[45]: Time 14.933278 seconds, bootstrap likelihood -116514.417446, best rearrangement setting 15
Bootstrap[46]: Time 15.135377 seconds, bootstrap likelihood -116873.717830, best rearrangement setting 14
Bootstrap[47]: Time 16.178207 seconds, bootstrap likelihood -116906.747446, best rearrangement setting 8
Bootstrap[48]: Time 15.763920 seconds, bootstrap likelihood -117484.897134, best rearrangement setting 6
Bootstrap[49]: Time 17.372234 seconds, bootstrap likelihood -117461.738129, best rearrangement setting 7
Bootstrap[50]: Time 6.792166 seconds, bootstrap likelihood -116585.284211, best rearrangement setting 7
Bootstrap[51]: Time 6.353969 seconds, bootstrap likelihood -115171.977160, best rearrangement setting 11
Bootstrap[52]: Time 15.672941 seconds, bootstrap likelihood -116850.241937, best rearrangement setting 12
Bootstrap[53]: Time 6.991697 seconds, bootstrap likelihood -117178.910099, best rearrangement setting 8
Bootstrap[54]: Time 15.574819 seconds, bootstrap likelihood -116435.823989, best rearrangement setting 9
Bootstrap[55]: Time 7.134227 seconds, bootstrap likelihood -116453.342667, best rearrangement setting 11
Bootstrap[56]: Time 6.823375 seconds, bootstrap likelihood -114802.085030, best rearrangement setting 5
Bootstrap[57]: Time 16.560223 seconds, bootstrap likelihood -115880.440385, best rearrangement setting 7
Bootstrap[58]: Time 15.943963 seconds, bootstrap likelihood -118530.438932, best rearrangement setting 10
Bootstrap[59]: Time 16.408773 seconds, bootstrap likelihood -116875.198083, best rearrangement setting 9
Bootstrap[60]: Time 14.718763 seconds, bootstrap likelihood -116918.294745, best rearrangement setting 7
Bootstrap[61]: Time 15.028837 seconds, bootstrap likelihood -116653.016056, best rearrangement setting 5
Bootstrap[62]: Time 15.296453 seconds, bootstrap likelihood -116239.263753, best rearrangement setting 11
Bootstrap[63]: Time 15.473294 seconds, bootstrap likelihood -115659.530615, best rearrangement setting 12
Bootstrap[64]: Time 15.283477 seconds, bootstrap likelihood -116588.004589, best rearrangement setting 7
Bootstrap[65]: Time 15.370203 seconds, bootstrap likelihood -117450.166730, best rearrangement setting 5
Bootstrap[66]: Time 6.677212 seconds, bootstrap likelihood -117302.013598, best rearrangement setting 5
Bootstrap[67]: Time 15.618836 seconds, bootstrap likelihood -116534.893012, best rearrangement setting 15
Bootstrap[68]: Time 15.131653 seconds, bootstrap likelihood -115725.354939, best rearrangement setting 11
Bootstrap[69]: Time 15.182677 seconds, bootstrap likelihood -116540.896761, best rearrangement setting 5
Bootstrap[70]: Time 16.162626 seconds, bootstrap likelihood -116294.013017, best rearrangement setting 8
Bootstrap[71]: Time 15.683569 seconds, bootstrap likelihood -116564.449761, best rearrangement setting 10
Bootstrap[72]: Time 15.707095 seconds, bootstrap likelihood -116078.353291, best rearrangement setting 11
Bootstrap[73]: Time 6.613641 seconds, bootstrap likelihood -116448.424921, best rearrangement setting 9
Bootstrap[74]: Time 15.666876 seconds, bootstrap likelihood -116295.276836, best rearrangement setting 5
Bootstrap[75]: Time 7.551274 seconds, bootstrap likelihood -116360.998571, best rearrangement setting 8
Bootstrap[76]: Time 15.369426 seconds, bootstrap likelihood -116464.137072, best rearrangement setting 9
Bootstrap[77]: Time 6.675339 seconds, bootstrap likelihood -116793.437934, best rearrangement setting 11
Bootstrap[78]: Time 6.586231 seconds, bootstrap likelihood -116463.443080, best rearrangement setting 15
Bootstrap[79]: Time 15.213779 seconds, bootstrap likelihood -116667.274688, best rearrangement setting 9
Bootstrap[80]: Time 6.452848 seconds, bootstrap likelihood -116622.791178, best rearrangement setting 15
Bootstrap[81]: Time 15.284941 seconds, bootstrap likelihood -115241.297737, best rearrangement setting 7
Bootstrap[82]: Time 14.152802 seconds, bootstrap likelihood -115317.518991, best rearrangement setting 6
Bootstrap[83]: Time 15.669058 seconds, bootstrap likelihood -116319.808216, best rearrangement setting 10
Bootstrap[84]: Time 15.150455 seconds, bootstrap likelihood -116750.952959, best rearrangement setting 11
Bootstrap[85]: Time 16.636421 seconds, bootstrap likelihood -116649.153515, best rearrangement setting 8
Bootstrap[86]: Time 15.999589 seconds, bootstrap likelihood -115824.605325, best rearrangement setting 7
Bootstrap[87]: Time 14.543294 seconds, bootstrap likelihood -115699.704420, best rearrangement setting 7
Bootstrap[88]: Time 15.303479 seconds, bootstrap likelihood -115909.840611, best rearrangement setting 12
Bootstrap[89]: Time 14.388359 seconds, bootstrap likelihood -116066.954321, best rearrangement setting 10
Bootstrap[90]: Time 6.856056 seconds, bootstrap likelihood -116564.374395, best rearrangement setting 8
Bootstrap[91]: Time 16.071160 seconds, bootstrap likelihood -117636.887081, best rearrangement setting 12
Bootstrap[92]: Time 6.798956 seconds, bootstrap likelihood -117314.521114, best rearrangement setting 13
Bootstrap[93]: Time 15.219411 seconds, bootstrap likelihood -114897.594595, best rearrangement setting 15
Bootstrap[94]: Time 14.866161 seconds, bootstrap likelihood -116904.105470, best rearrangement setting 5
Bootstrap[95]: Time 15.486989 seconds, bootstrap likelihood -116106.717531, best rearrangement setting 5
Bootstrap[96]: Time 15.570479 seconds, bootstrap likelihood -116881.456186, best rearrangement setting 13
Bootstrap[97]: Time 15.568816 seconds, bootstrap likelihood -117595.653997, best rearrangement setting 11
Bootstrap[98]: Time 16.117093 seconds, bootstrap likelihood -115576.968781, best rearrangement setting 6
Bootstrap[99]: Time 14.834300 seconds, bootstrap likelihood -117592.796928, best rearrangement setting 14


Overall Time for 100 Rapid Bootstraps 1497.036889 seconds
Average Time per Rapid Bootstrap 14.970369 seconds

Starting ML Search ...


Printed linked AA GTR matrix that achieved an overall improvement of 1574.075365 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 67.617600 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 3.052824 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.132404 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.014960 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided

Fast ML optimization finished

Fast ML search Time: 1418.062076 seconds


Printed linked AA GTR matrix that achieved an overall improvement of 1570.897611 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 67.402569 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 3.036381 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.129116 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.014606 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided

Slow ML Search 0 Likelihood: -116561.727264
Slow ML Search 1 Likelihood: -116561.727264
Slow ML Search 2 Likelihood: -116561.727264
Slow ML Search 3 Likelihood: -116561.727261
Slow ML Search 4 Likelihood: -116561.727262
Slow ML Search 5 Likelihood: -116561.727262
Slow ML Search 6 Likelihood: -116561.727262
Slow ML Search 7 Likelihood: -116561.727261
Slow ML Search 8 Likelihood: -116561.727261
Slow ML Search 9 Likelihood: -116561.727262
Slow ML optimization finished

Slow ML search Time: 861.647170 seconds

Printed linked AA GTR matrix that achieved an overall improvement of 1570.716196 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 67.160013 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 3.032687 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.131075 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.015003 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov_Partition_No Name Provided

Thorough ML search Time: 364.521617 seconds

Final ML Optimization Likelihood: -116561.729206

Model Information:

Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA
alpha: 0.611169
Tree-Length: 5.497023
rate A <-> R: 0.374121
rate A <-> N: 0.717828
rate A <-> D: 1.837016
rate A <-> C: 3.903701
rate A <-> Q: 0.202097
rate A <-> E: 2.816313
rate A <-> G: 4.910246
rate A <-> H: 0.066124
rate A <-> I: 1.961841
rate A <-> L: 1.204552
rate A <-> K: 0.159646
rate A <-> M: 0.886599
rate A <-> F: 1.181818
rate A <-> P: 4.353826
rate A <-> S: 23.253324
rate A <-> T: 14.091943
rate A <-> W: 0.000000
rate A <-> Y: 0.059395
rate A <-> V: 13.889210
rate R <-> N: 0.392034
rate R <-> D: 0.000000
rate R <-> C: 0.746875
rate R <-> Q: 5.583847
rate R <-> E: 0.762358
rate R <-> G: 1.099634
rate R <-> H: 3.126057
rate R <-> I: 0.228724
rate R <-> L: 0.430640
rate R <-> K: 23.706652
rate R <-> M: 0.959927
rate R <-> F: 0.193855
rate R <-> P: 0.237316
rate R <-> S: 1.220255
rate R <-> T: 0.540917
rate R <-> W: 0.698630
rate R <-> Y: 0.215265
rate R <-> V: 0.000000
rate N <-> D: 15.288364
rate N <-> C: 1.044236
rate N <-> Q: 7.502531
rate N <-> E: 3.340419
rate N <-> G: 2.531565
rate N <-> H: 9.547049
rate N <-> I: 2.085497
rate N <-> L: 0.840013
rate N <-> K: 8.650791
rate N <-> M: 0.879357
rate N <-> F: 0.433395
rate N <-> P: 0.369542
rate N <-> S: 16.037654
rate N <-> T: 8.946939
rate N <-> W: 0.260131
rate N <-> Y: 3.555640
rate N <-> V: 0.476766
rate D <-> C: 0.761536
rate D <-> Q: 0.000000
rate D <-> E: 32.251726
rate D <-> G: 2.363138
rate D <-> H: 1.709070
rate D <-> I: 0.154095
rate D <-> L: 0.162305
rate D <-> K: 0.941061
rate D <-> M: 0.058005
rate D <-> F: 0.064853
rate D <-> P: 0.674538
rate D <-> S: 3.070006
rate D <-> T: 1.357683
rate D <-> W: 0.244720
rate D <-> Y: 0.722561
rate D <-> V: 0.309415
rate C <-> Q: 0.000000
rate C <-> E: 0.274913
rate C <-> G: 2.979403
rate C <-> H: 2.597679
rate C <-> I: 0.815281
rate C <-> L: 1.432912
rate C <-> K: 0.000000
rate C <-> M: 1.901331
rate C <-> F: 1.865620
rate C <-> P: 0.000000
rate C <-> S: 11.417831
rate C <-> T: 2.881137
rate C <-> W: 0.507437
rate C <-> Y: 3.948894
rate C <-> V: 4.549705
rate Q <-> E: 7.905191
rate Q <-> G: 0.000000
rate Q <-> H: 20.565072
rate Q <-> I: 0.380117
rate Q <-> L: 1.728220
rate Q <-> K: 6.293046
rate Q <-> M: 0.931097
rate Q <-> F: 0.227509
rate Q <-> P: 3.062256
rate Q <-> S: 1.891475
rate Q <-> T: 1.655169
rate Q <-> W: 0.000000
rate Q <-> Y: 1.499081
rate Q <-> V: 0.000000
rate E <-> G: 2.194776
rate E <-> H: 0.139541
rate E <-> I: 0.181419
rate E <-> L: 0.444611
rate E <-> K: 4.055635
rate E <-> M: 0.000000
rate E <-> F: 0.195938
rate E <-> P: 0.194216
rate E <-> S: 2.372822
rate E <-> T: 1.723371
rate E <-> W: 0.201300
rate E <-> Y: 0.824964
rate E <-> V: 0.554422
rate G <-> H: 0.746734
rate G <-> I: 0.125365
rate G <-> L: 0.032154
rate G <-> K: 0.299323
rate G <-> M: 0.112962
rate G <-> F: 0.259684
rate G <-> P: 0.124785
rate G <-> S: 6.076219
rate G <-> T: 0.205760
rate G <-> W: 0.649583
rate G <-> Y: 0.000000
rate G <-> V: 0.543076
rate H <-> I: 0.099150
rate H <-> L: 0.888566
rate H <-> K: 0.267001
rate H <-> M: 0.000000
rate H <-> F: 0.711626
rate H <-> P: 0.348869
rate H <-> S: 1.731975
rate H <-> T: 1.412846
rate H <-> W: 0.000000
rate H <-> Y: 11.915816
rate H <-> V: 0.000000
rate I <-> L: 17.523256
rate I <-> K: 1.187946
rate I <-> M: 15.932970
rate I <-> F: 3.155328
rate I <-> P: 0.104400
rate I <-> S: 1.049349
rate I <-> T: 8.473903
rate I <-> W: 0.470872
rate I <-> Y: 1.758434
rate I <-> V: 51.690519
rate L <-> K: 0.656748
rate L <-> M: 13.061391
rate L <-> F: 6.219782
rate L <-> P: 0.993062
rate L <-> S: 1.755787
rate L <-> T: 1.596442
rate L <-> W: 1.303612
rate L <-> Y: 1.125180
rate L <-> V: 4.541107
rate K <-> M: 0.678777
rate K <-> F: 0.111165
rate K <-> P: 0.375126
rate K <-> S: 1.979836
rate K <-> T: 1.806050
rate K <-> W: 0.174713
rate K <-> Y: 0.640916
rate K <-> V: 0.261877
rate M <-> F: 1.274708
rate M <-> P: 0.196147
rate M <-> S: 0.718446
rate M <-> T: 5.631946
rate M <-> W: 0.381893
rate M <-> Y: 0.303230
rate M <-> V: 6.970158
rate F <-> P: 0.202451
rate F <-> S: 1.294535
rate F <-> T: 0.595678
rate F <-> W: 0.933784
rate F <-> Y: 10.671196
rate F <-> V: 1.306016
rate P <-> S: 5.718686
rate P <-> T: 3.032239
rate P <-> W: 0.543919
rate P <-> Y: 0.696467
rate P <-> V: 0.691008
rate S <-> T: 22.940521
rate S <-> W: 0.289372
rate S <-> Y: 1.450033
rate S <-> V: 1.289762
rate T <-> W: 0.000000
rate T <-> Y: 1.166332
rate T <-> V: 11.938505
rate W <-> Y: 1.556314
rate W <-> V: 0.000000
rate Y <-> V: 1.000000

freq pi(A): 0.043508
freq pi(R): 0.038292
freq pi(N): 0.062483
freq pi(D): 0.027575
freq pi(C): 0.013206
freq pi(Q): 0.017035
freq pi(E): 0.032910
freq pi(G): 0.040615
freq pi(H): 0.017320
freq pi(I): 0.076552
freq pi(L): 0.121089
freq pi(K): 0.081894
freq pi(M): 0.018295
freq pi(F): 0.138937
freq pi(P): 0.021362
freq pi(S): 0.074952
freq pi(T): 0.046781
freq pi(W): 0.015991
freq pi(Y): 0.054417
freq pi(V): 0.056786


ML search took 2644.324432 secs or 0.734535 hours

Combined Bootstrap and ML search took 4141.364726 secs or 1.150379 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-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov



Found 1 tree in File /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov

Program execution info written to /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov
All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bootstrap.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov

Best-scoring ML tree written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov

Best-scoring ML tree with support values written to: /N/dc2/projects/marinovg/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitions.RAxML-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_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-PROTGAMMAGTR-supermatrix.mito.full-assemblies.Oligohymenophorea.95perc_cov

Overall execution time for full ML analysis: 4141.438767 secs or 1.150400 hours or 0.047933 days