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 9 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 10 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 11 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 12 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 62 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 63 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 64 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 65 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 66 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 75 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 76 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 77 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 78 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 271 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 272 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 273 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 274 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 441 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 455 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 456 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 457 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 481 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 482 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 488 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 489 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 490 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 491 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 492 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 493 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 494 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 495 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 496 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 497 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 498 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 499 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 500 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 501 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 502 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 503 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 504 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 517 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 518 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 519 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 520 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 521 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 522 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 523 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 524 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 525 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 526 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 527 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 528 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 529 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 530 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 531 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 532 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 533 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 534 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 535 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 536 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 537 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 538 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 539 contains only undetermined values which will be treated as missing data


IMPORTANT WARNING: Sequences P_multimicronucleatum-Sample_M04_60aa-ORF_renamed_min100aa_ORF and P_multimicronucleatum-Sample_M05_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_caudatum-Sample_C065_60aa-ORF_renamed_min100aa_ORF and P_caudatum-Sample_C104_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_tetraurelia-Sample_291_60aa-ORF_renamed_min100aa_ORF and P_tetraurelia-Sample_99_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_sexaurelia-Sample_132_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_133_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_sexaurelia-Sample_134_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_137_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_128_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_sexaurelia-Sample_126_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_Indo1-7I_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_sexaurelia-Sample_127_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_131_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_sexaurelia-Sample_127_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_Moz13BIII_60aa-ORF_renamed_min100aa_ORF are exactly identical

IMPORTANT WARNING
Found 9 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.


IMPORTANT WARNING
Found 71 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 
sequence duplicates and undetermined columns removed is printed to file cob.renamed.muscle.Oligohymenophorea.fa.reduced


This is RAxML version 8.1.3 released by Alexandros Stamatakis on August 13 2014.

With greatly appreciated code contributions by:
Andre Aberer      (HITS)
Simon Berger      (HITS)
Alexey Kozlov     (HITS)
Kassian Kobert    (HITS)
David Dao         (KIT and HITS)
Nick Pattengale   (Sandia)
Wayne Pfeiffer    (SDSC)
Akifumi S. Tanabe (NRIFS)

Alignment has 264 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 18.16%

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: 264
Name: No Name Provided
DataType: AA
Substitution Matrix: GTR
Using empirical base frequencies




RAxML was called as follows:

raxml -f a -s cob.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 



Printed linked AA GTR matrix that achieved an overall improvement of 160.808066 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 9.018122 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.499449 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Time for BS model parameter optimization 17.118211
Bootstrap[0]: Time 18.524585 seconds, bootstrap likelihood -3770.340998, best rearrangement setting 13
Bootstrap[1]: Time 1.504144 seconds, bootstrap likelihood -3964.232841, best rearrangement setting 13
Bootstrap[2]: Time 1.527804 seconds, bootstrap likelihood -3713.327092, best rearrangement setting 12
Bootstrap[3]: Time 1.408227 seconds, bootstrap likelihood -3725.849587, best rearrangement setting 15
Bootstrap[4]: Time 1.470083 seconds, bootstrap likelihood -3703.531919, best rearrangement setting 10
Bootstrap[5]: Time 1.500734 seconds, bootstrap likelihood -3734.914553, best rearrangement setting 10
Bootstrap[6]: Time 1.393908 seconds, bootstrap likelihood -3913.530529, best rearrangement setting 6
Bootstrap[7]: Time 1.535480 seconds, bootstrap likelihood -4043.074051, best rearrangement setting 14
Bootstrap[8]: Time 1.351909 seconds, bootstrap likelihood -3651.533537, best rearrangement setting 5
Bootstrap[9]: Time 1.383237 seconds, bootstrap likelihood -3608.575265, best rearrangement setting 7
Bootstrap[10]: Time 1.329700 seconds, bootstrap likelihood -3799.149960, best rearrangement setting 7
Bootstrap[11]: Time 1.464713 seconds, bootstrap likelihood -3970.687740, best rearrangement setting 5
Bootstrap[12]: Time 1.453312 seconds, bootstrap likelihood -3859.903231, best rearrangement setting 8
Bootstrap[13]: Time 1.481364 seconds, bootstrap likelihood -4017.847004, best rearrangement setting 7
Bootstrap[14]: Time 1.359820 seconds, bootstrap likelihood -3687.718868, best rearrangement setting 12
Bootstrap[15]: Time 1.350450 seconds, bootstrap likelihood -3831.311634, best rearrangement setting 15
Bootstrap[16]: Time 1.435370 seconds, bootstrap likelihood -3713.386631, best rearrangement setting 12
Bootstrap[17]: Time 1.244257 seconds, bootstrap likelihood -3675.709260, best rearrangement setting 12
Bootstrap[18]: Time 1.223145 seconds, bootstrap likelihood -3821.925845, best rearrangement setting 5
Bootstrap[19]: Time 1.446999 seconds, bootstrap likelihood -3784.573563, best rearrangement setting 8
Bootstrap[20]: Time 1.524197 seconds, bootstrap likelihood -3705.013618, best rearrangement setting 10
Bootstrap[21]: Time 1.395462 seconds, bootstrap likelihood -3831.377461, best rearrangement setting 6
Bootstrap[22]: Time 1.445948 seconds, bootstrap likelihood -3826.612119, best rearrangement setting 5
Bootstrap[23]: Time 1.262147 seconds, bootstrap likelihood -3847.356044, best rearrangement setting 7
Bootstrap[24]: Time 1.238547 seconds, bootstrap likelihood -3752.327303, best rearrangement setting 8
Bootstrap[25]: Time 1.191753 seconds, bootstrap likelihood -3625.613362, best rearrangement setting 6
Bootstrap[26]: Time 1.344874 seconds, bootstrap likelihood -3887.897145, best rearrangement setting 12
Bootstrap[27]: Time 1.444651 seconds, bootstrap likelihood -3681.199358, best rearrangement setting 10
Bootstrap[28]: Time 1.355618 seconds, bootstrap likelihood -3737.388896, best rearrangement setting 11
Bootstrap[29]: Time 1.527393 seconds, bootstrap likelihood -3837.146008, best rearrangement setting 12
Bootstrap[30]: Time 1.205672 seconds, bootstrap likelihood -3743.954131, best rearrangement setting 15
Bootstrap[31]: Time 1.201829 seconds, bootstrap likelihood -3845.638586, best rearrangement setting 15
Bootstrap[32]: Time 1.289342 seconds, bootstrap likelihood -3494.193134, best rearrangement setting 6
Bootstrap[33]: Time 1.439872 seconds, bootstrap likelihood -3594.332033, best rearrangement setting 15
Bootstrap[34]: Time 1.237546 seconds, bootstrap likelihood -3934.761320, best rearrangement setting 11
Bootstrap[35]: Time 1.146620 seconds, bootstrap likelihood -3631.161586, best rearrangement setting 8
Bootstrap[36]: Time 1.383856 seconds, bootstrap likelihood -3671.131266, best rearrangement setting 9
Bootstrap[37]: Time 1.240510 seconds, bootstrap likelihood -3914.170358, best rearrangement setting 11
Bootstrap[38]: Time 1.483126 seconds, bootstrap likelihood -4103.089123, best rearrangement setting 8
Bootstrap[39]: Time 1.548785 seconds, bootstrap likelihood -3751.378892, best rearrangement setting 13
Bootstrap[40]: Time 1.230294 seconds, bootstrap likelihood -3575.759763, best rearrangement setting 13
Bootstrap[41]: Time 1.614998 seconds, bootstrap likelihood -3941.108792, best rearrangement setting 10
Bootstrap[42]: Time 1.371278 seconds, bootstrap likelihood -3717.361532, best rearrangement setting 5
Bootstrap[43]: Time 1.479632 seconds, bootstrap likelihood -3842.013666, best rearrangement setting 14
Bootstrap[44]: Time 1.257203 seconds, bootstrap likelihood -3843.862174, best rearrangement setting 10
Bootstrap[45]: Time 1.208543 seconds, bootstrap likelihood -3726.919369, best rearrangement setting 15
Bootstrap[46]: Time 1.176326 seconds, bootstrap likelihood -3629.731809, best rearrangement setting 14
Bootstrap[47]: Time 1.476107 seconds, bootstrap likelihood -3867.992680, best rearrangement setting 8
Bootstrap[48]: Time 1.583819 seconds, bootstrap likelihood -3607.320399, best rearrangement setting 6
Bootstrap[49]: Time 1.278137 seconds, bootstrap likelihood -3850.769738, best rearrangement setting 7
Bootstrap[50]: Time 1.338813 seconds, bootstrap likelihood -3909.118644, best rearrangement setting 7
Bootstrap[51]: Time 1.251976 seconds, bootstrap likelihood -3969.107677, best rearrangement setting 11
Bootstrap[52]: Time 1.172710 seconds, bootstrap likelihood -4087.140207, best rearrangement setting 12
Bootstrap[53]: Time 1.257856 seconds, bootstrap likelihood -3609.866445, best rearrangement setting 8
Bootstrap[54]: Time 1.216483 seconds, bootstrap likelihood -3863.788688, best rearrangement setting 9
Bootstrap[55]: Time 1.234224 seconds, bootstrap likelihood -3736.183928, best rearrangement setting 11
Bootstrap[56]: Time 1.212372 seconds, bootstrap likelihood -3813.727394, best rearrangement setting 5
Bootstrap[57]: Time 1.222050 seconds, bootstrap likelihood -3749.439743, best rearrangement setting 7
Bootstrap[58]: Time 1.217155 seconds, bootstrap likelihood -3484.882680, best rearrangement setting 10
Bootstrap[59]: Time 1.137301 seconds, bootstrap likelihood -3639.746243, best rearrangement setting 9
Bootstrap[60]: Time 1.254576 seconds, bootstrap likelihood -3727.102438, best rearrangement setting 7
Bootstrap[61]: Time 1.268710 seconds, bootstrap likelihood -3914.086184, best rearrangement setting 5
Bootstrap[62]: Time 1.314565 seconds, bootstrap likelihood -3694.948183, best rearrangement setting 11
Bootstrap[63]: Time 1.509025 seconds, bootstrap likelihood -3551.597044, best rearrangement setting 12
Bootstrap[64]: Time 1.460589 seconds, bootstrap likelihood -4074.041256, best rearrangement setting 7
Bootstrap[65]: Time 1.404666 seconds, bootstrap likelihood -3765.154773, best rearrangement setting 5
Bootstrap[66]: Time 1.133242 seconds, bootstrap likelihood -3549.641707, best rearrangement setting 5
Bootstrap[67]: Time 1.426266 seconds, bootstrap likelihood -3791.264571, best rearrangement setting 15
Bootstrap[68]: Time 1.394318 seconds, bootstrap likelihood -3500.071344, best rearrangement setting 11
Bootstrap[69]: Time 1.713802 seconds, bootstrap likelihood -3813.892261, best rearrangement setting 5
Bootstrap[70]: Time 1.468563 seconds, bootstrap likelihood -4116.136382, best rearrangement setting 8
Bootstrap[71]: Time 1.301087 seconds, bootstrap likelihood -3519.031946, best rearrangement setting 10
Bootstrap[72]: Time 1.331939 seconds, bootstrap likelihood -3750.880445, best rearrangement setting 11
Bootstrap[73]: Time 1.363112 seconds, bootstrap likelihood -3966.141407, best rearrangement setting 9
Bootstrap[74]: Time 1.101245 seconds, bootstrap likelihood -3639.881220, best rearrangement setting 5
Bootstrap[75]: Time 1.733648 seconds, bootstrap likelihood -3604.854147, best rearrangement setting 8
Bootstrap[76]: Time 1.479342 seconds, bootstrap likelihood -3552.229920, best rearrangement setting 9
Bootstrap[77]: Time 1.210717 seconds, bootstrap likelihood -3689.600293, best rearrangement setting 11
Bootstrap[78]: Time 1.477293 seconds, bootstrap likelihood -3994.107698, best rearrangement setting 15
Bootstrap[79]: Time 1.548666 seconds, bootstrap likelihood -3865.946383, best rearrangement setting 9
Bootstrap[80]: Time 1.205724 seconds, bootstrap likelihood -3685.267297, best rearrangement setting 15
Bootstrap[81]: Time 1.034906 seconds, bootstrap likelihood -3278.610371, best rearrangement setting 7
Bootstrap[82]: Time 1.590489 seconds, bootstrap likelihood -3669.855587, best rearrangement setting 6
Bootstrap[83]: Time 1.395640 seconds, bootstrap likelihood -3769.315428, best rearrangement setting 10
Bootstrap[84]: Time 1.510544 seconds, bootstrap likelihood -3649.502670, best rearrangement setting 11
Bootstrap[85]: Time 1.378368 seconds, bootstrap likelihood -3928.483290, best rearrangement setting 8
Bootstrap[86]: Time 1.427946 seconds, bootstrap likelihood -3726.310643, best rearrangement setting 7
Bootstrap[87]: Time 1.463534 seconds, bootstrap likelihood -3650.647818, best rearrangement setting 7
Bootstrap[88]: Time 1.397472 seconds, bootstrap likelihood -3775.262266, best rearrangement setting 12
Bootstrap[89]: Time 1.526947 seconds, bootstrap likelihood -3735.279909, best rearrangement setting 10
Bootstrap[90]: Time 1.134087 seconds, bootstrap likelihood -3952.118303, best rearrangement setting 8
Bootstrap[91]: Time 1.304442 seconds, bootstrap likelihood -3735.381816, best rearrangement setting 12
Bootstrap[92]: Time 1.373648 seconds, bootstrap likelihood -3705.075416, best rearrangement setting 13
Bootstrap[93]: Time 1.422547 seconds, bootstrap likelihood -4051.294643, best rearrangement setting 15
Bootstrap[94]: Time 1.215020 seconds, bootstrap likelihood -3772.934461, best rearrangement setting 5
Bootstrap[95]: Time 1.351387 seconds, bootstrap likelihood -3747.012268, best rearrangement setting 5
Bootstrap[96]: Time 1.333510 seconds, bootstrap likelihood -3428.003091, best rearrangement setting 13
Bootstrap[97]: Time 1.231152 seconds, bootstrap likelihood -3625.374276, best rearrangement setting 11
Bootstrap[98]: Time 1.200578 seconds, bootstrap likelihood -3856.681382, best rearrangement setting 6
Bootstrap[99]: Time 1.242449 seconds, bootstrap likelihood -3800.560846, best rearrangement setting 14


Overall Time for 100 Rapid Bootstraps 153.033955 seconds
Average Time per Rapid Bootstrap 1.530340 seconds

Starting ML Search ...


Printed linked AA GTR matrix that achieved an overall improvement of 164.377521 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 8.038273 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.388075 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.044163 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided

Fast ML optimization finished

Fast ML search Time: 118.185267 seconds


Printed linked AA GTR matrix that achieved an overall improvement of 161.949465 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 8.131886 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.380051 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.039268 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided

Slow ML Search 0 Likelihood: -3816.647921
Slow ML Search 1 Likelihood: -3816.647922
Slow ML Search 2 Likelihood: -3816.647921
Slow ML Search 3 Likelihood: -3816.647921
Slow ML Search 4 Likelihood: -3816.647921
Slow ML Search 5 Likelihood: -3816.647921
Slow ML Search 6 Likelihood: -3816.648151
Slow ML Search 7 Likelihood: -3816.647921
Slow ML Search 8 Likelihood: -3816.647921
Slow ML Search 9 Likelihood: -3816.647921
Slow ML optimization finished

Slow ML search Time: 119.981183 seconds

Printed linked AA GTR matrix that achieved an overall improvement of 161.822806 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 8.221491 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.377701 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.038986 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_proteinGTRmodel.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea_Partition_No Name Provided

Thorough ML search Time: 26.239389 seconds

Final ML Optimization Likelihood: -3816.025235

Model Information:

Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA
alpha: 0.498019
Tree-Length: 2.439751
rate A <-> R: 0.000000
rate A <-> N: 2.962148
rate A <-> D: 0.000000
rate A <-> C: 7.901160
rate A <-> Q: 0.000000
rate A <-> E: 0.000000
rate A <-> G: 0.000000
rate A <-> H: 0.000000
rate A <-> I: 1.136118
rate A <-> L: 0.000000
rate A <-> K: 1.036927
rate A <-> M: 1.172171
rate A <-> F: 1.497563
rate A <-> P: 0.000000
rate A <-> S: 32.122971
rate A <-> T: 8.485213
rate A <-> W: 0.000000
rate A <-> Y: 2.358628
rate A <-> V: 12.583972
rate R <-> N: 0.000000
rate R <-> D: 0.000000
rate R <-> C: 0.000000
rate R <-> Q: 17.304508
rate R <-> E: 0.471229
rate R <-> G: 0.000000
rate R <-> H: 0.000000
rate R <-> I: 0.000000
rate R <-> L: 0.000000
rate R <-> K: 45.057353
rate R <-> M: 0.000000
rate R <-> F: 0.000000
rate R <-> P: 0.000000
rate R <-> S: 0.000000
rate R <-> T: 4.452921
rate R <-> W: 0.000000
rate R <-> Y: 0.000000
rate R <-> V: 0.000000
rate N <-> D: 1.887139
rate N <-> C: 5.881880
rate N <-> Q: 0.000000
rate N <-> E: 0.000000
rate N <-> G: 1.670623
rate N <-> H: 1.807630
rate N <-> I: 1.556654
rate N <-> L: 0.000000
rate N <-> K: 9.489242
rate N <-> M: 0.000000
rate N <-> F: 0.053330
rate N <-> P: 6.119930
rate N <-> S: 19.913526
rate N <-> T: 5.120201
rate N <-> W: 1.443752
rate N <-> Y: 0.541357
rate N <-> V: 5.978797
rate D <-> C: 0.000000
rate D <-> Q: 0.000000
rate D <-> E: 23.153086
rate D <-> G: 1.061663
rate D <-> H: 1.708852
rate D <-> I: 0.000000
rate D <-> L: 0.000000
rate D <-> K: 2.456950
rate D <-> M: 0.000000
rate D <-> F: 0.000000
rate D <-> P: 0.000000
rate D <-> S: 1.986926
rate D <-> T: 0.000000
rate D <-> W: 1.708035
rate D <-> Y: 0.000000
rate D <-> V: 0.000000
rate C <-> Q: 0.000000
rate C <-> E: 0.000000
rate C <-> G: 0.000000
rate C <-> H: 0.000000
rate C <-> I: 0.000000
rate C <-> L: 3.563593
rate C <-> K: 0.000000
rate C <-> M: 0.000000
rate C <-> F: 8.130453
rate C <-> P: 0.000000
rate C <-> S: 12.459380
rate C <-> T: 0.000000
rate C <-> W: 6.593905
rate C <-> Y: 0.000000
rate C <-> V: 0.000000
rate Q <-> E: 11.174190
rate Q <-> G: 0.000000
rate Q <-> H: 20.116388
rate Q <-> I: 0.000000
rate Q <-> L: 1.753753
rate Q <-> K: 0.000000
rate Q <-> M: 0.000000
rate Q <-> F: 1.266316
rate Q <-> P: 0.000000
rate Q <-> S: 3.910116
rate Q <-> T: 6.051861
rate Q <-> W: 0.000000
rate Q <-> Y: 3.414243
rate Q <-> V: 0.332370
rate E <-> G: 1.075976
rate E <-> H: 0.000000
rate E <-> I: 0.933040
rate E <-> L: 0.000000
rate E <-> K: 0.000000
rate E <-> M: 0.000000
rate E <-> F: 0.000000
rate E <-> P: 0.916839
rate E <-> S: 0.000000
rate E <-> T: 0.000000
rate E <-> W: 0.000000
rate E <-> Y: 0.215152
rate E <-> V: 0.000000
rate G <-> H: 1.479854
rate G <-> I: 0.000000
rate G <-> L: 0.000000
rate G <-> K: 0.000000
rate G <-> M: 0.000000
rate G <-> F: 0.000000
rate G <-> P: 0.000000
rate G <-> S: 6.991295
rate G <-> T: 0.000000
rate G <-> W: 1.634511
rate G <-> Y: 0.000000
rate G <-> V: 0.000000
rate H <-> I: 0.000000
rate H <-> L: 0.683022
rate H <-> K: 2.187680
rate H <-> M: 0.000000
rate H <-> F: 0.000000
rate H <-> P: 0.000000
rate H <-> S: 0.000000
rate H <-> T: 0.000000
rate H <-> W: 0.000000
rate H <-> Y: 5.720056
rate H <-> V: 0.000000
rate I <-> L: 22.766681
rate I <-> K: 0.000000
rate I <-> M: 7.636010
rate I <-> F: 5.052393
rate I <-> P: 2.267447
rate I <-> S: 2.086170
rate I <-> T: 15.113571
rate I <-> W: 0.000000
rate I <-> Y: 5.773680
rate I <-> V: 69.660584
rate L <-> K: 0.000000
rate L <-> M: 11.428897
rate L <-> F: 3.050618
rate L <-> P: 0.748320
rate L <-> S: 2.934144
rate L <-> T: 0.000000
rate L <-> W: 0.702521
rate L <-> Y: 0.184365
rate L <-> V: 5.418323
rate K <-> M: 3.709120
rate K <-> F: 0.410567
rate K <-> P: 1.182829
rate K <-> S: 3.960699
rate K <-> T: 3.638172
rate K <-> W: 0.000000
rate K <-> Y: 3.548604
rate K <-> V: 0.000000
rate M <-> F: 2.370519
rate M <-> P: 0.000000
rate M <-> S: 0.000000
rate M <-> T: 5.369688
rate M <-> W: 0.000000
rate M <-> Y: 4.186611
rate M <-> V: 12.047450
rate F <-> P: 0.000000
rate F <-> S: 0.000000
rate F <-> T: 0.468695
rate F <-> W: 2.654527
rate F <-> Y: 8.723943
rate F <-> V: 0.000000
rate P <-> S: 7.027612
rate P <-> T: 1.962852
rate P <-> W: 2.929159
rate P <-> Y: 0.000000
rate P <-> V: 0.000000
rate S <-> T: 16.655160
rate S <-> W: 0.000000
rate S <-> Y: 0.000000
rate S <-> V: 0.000000
rate T <-> W: 0.000000
rate T <-> Y: 0.000000
rate T <-> V: 16.806806
rate W <-> Y: 0.000000
rate W <-> V: 0.000000
rate Y <-> V: 1.000000

freq pi(A): 0.041286
freq pi(R): 0.027822
freq pi(N): 0.045270
freq pi(D): 0.043072
freq pi(C): 0.013396
freq pi(Q): 0.016899
freq pi(E): 0.043759
freq pi(G): 0.047949
freq pi(H): 0.029402
freq pi(I): 0.064780
freq pi(L): 0.122072
freq pi(K): 0.039294
freq pi(M): 0.021983
freq pi(F): 0.142886
freq pi(P): 0.025898
freq pi(S): 0.063200
freq pi(T): 0.059490
freq pi(W): 0.026860
freq pi(Y): 0.063200
freq pi(V): 0.061482


ML search took 264.531056 secs or 0.073481 hours

Combined Bootstrap and ML search took 417.565967 secs or 0.115991 hours

Drawing Bootstrap Support Values on best-scoring ML tree ...



Found 1 tree in File /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea



Found 1 tree in File /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea

Program execution info written to /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea
All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bootstrap.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea

Best-scoring ML tree written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea

Best-scoring ML tree with support values written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitions.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea

Best-scoring ML tree with support values as branch labels written to: /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bipartitionsBranchLabels.RAxML-PROTGAMMAGTR-cob.renamed.muscle.Oligohymenophorea

Overall execution time for full ML analysis: 417.582411 secs or 0.115995 hours or 0.004833 days