IMPORTANT WARNING: Alignment column 187 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 197 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 270 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 334 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 335 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 336 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 337 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 338 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 339 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 340 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 363 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 364 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 365 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 366 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 367 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 379 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 380 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 381 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 382 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 383 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 384 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 385 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 386 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 387 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 388 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 389 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 390 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 391 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 392 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 393 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 394 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 395 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 396 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 397 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 398 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 399 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 400 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 401 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 402 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 403 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 404 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 405 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 406 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 407 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 408 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 409 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 410 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 411 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 412 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 413 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 414 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 415 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 416 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 417 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 418 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 419 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 420 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 421 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 422 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 423 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 424 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 442 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 443 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 444 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 445 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 446 contains only undetermined values which will be treated as missing data


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_131_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_134_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_sexaurelia-Sample_131_60aa-ORF_renamed_min100aa_ORF and P_sexaurelia-Sample_137_60aa-ORF_renamed_min100aa_ORF are exactly identical


IMPORTANT WARNING: Sequences P_biaurelia-Sample_379_60aa-ORF_renamed_min100aa_ORF and P_biaurelia-Sample_USBL-36I1_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_tetraurelia-Sample_291_60aa-ORF_renamed_min100aa_ORF and P_tetraurelia-Sample_A_60aa-ORF_renamed_min100aa_ORF are exactly identical

IMPORTANT WARNING
Found 6 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.


IMPORTANT WARNING
Found 66 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 nad1a.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 224 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 27.77%

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: 224
Name: No Name Provided
DataType: AA
Substitution Matrix: GTR
Using empirical base frequencies




RAxML was called as follows:

raxml -f a -s nad1a.renamed.muscle.Oligohymenophorea.fa -n RAxML-PROTGAMMAGTR-nad1a.renamed.muscle.Oligohymenophorea -m PROTGAMMAGTR -T 16 -p 12345 -N 100 -x 12345 



Printed linked AA GTR matrix that achieved an overall improvement of 177.442125 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 14.471969 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.606175 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Time for BS model parameter optimization 15.836453
Bootstrap[0]: Time 17.274148 seconds, bootstrap likelihood -3600.129763, best rearrangement setting 13
Bootstrap[1]: Time 1.259577 seconds, bootstrap likelihood -3394.536031, best rearrangement setting 13
Bootstrap[2]: Time 1.718401 seconds, bootstrap likelihood -3648.361027, best rearrangement setting 12
Bootstrap[3]: Time 1.202836 seconds, bootstrap likelihood -3370.362537, best rearrangement setting 15
Bootstrap[4]: Time 1.301758 seconds, bootstrap likelihood -3809.118401, best rearrangement setting 10
Bootstrap[5]: Time 1.162855 seconds, bootstrap likelihood -3341.577905, best rearrangement setting 10
Bootstrap[6]: Time 1.182891 seconds, bootstrap likelihood -3148.372112, best rearrangement setting 6
Bootstrap[7]: Time 1.337044 seconds, bootstrap likelihood -3217.444582, best rearrangement setting 14
Bootstrap[8]: Time 1.312751 seconds, bootstrap likelihood -3199.987730, best rearrangement setting 5
Bootstrap[9]: Time 1.267108 seconds, bootstrap likelihood -3321.002153, best rearrangement setting 7
Bootstrap[10]: Time 1.217848 seconds, bootstrap likelihood -3525.136440, best rearrangement setting 7
Bootstrap[11]: Time 1.651172 seconds, bootstrap likelihood -3323.773364, best rearrangement setting 5
Bootstrap[12]: Time 1.375339 seconds, bootstrap likelihood -3490.424207, best rearrangement setting 8
Bootstrap[13]: Time 1.596810 seconds, bootstrap likelihood -3449.864756, best rearrangement setting 7
Bootstrap[14]: Time 1.594265 seconds, bootstrap likelihood -3148.976299, best rearrangement setting 12
Bootstrap[15]: Time 1.587923 seconds, bootstrap likelihood -3369.676886, best rearrangement setting 15
Bootstrap[16]: Time 1.497848 seconds, bootstrap likelihood -3559.973389, best rearrangement setting 12
Bootstrap[17]: Time 1.471274 seconds, bootstrap likelihood -3442.925038, best rearrangement setting 12
Bootstrap[18]: Time 1.334276 seconds, bootstrap likelihood -3710.904930, best rearrangement setting 5
Bootstrap[19]: Time 1.747422 seconds, bootstrap likelihood -3406.725505, best rearrangement setting 8
Bootstrap[20]: Time 1.538888 seconds, bootstrap likelihood -3340.549074, best rearrangement setting 10
Bootstrap[21]: Time 1.584794 seconds, bootstrap likelihood -3198.927675, best rearrangement setting 6
Bootstrap[22]: Time 1.463843 seconds, bootstrap likelihood -3188.830987, best rearrangement setting 5
Bootstrap[23]: Time 1.174860 seconds, bootstrap likelihood -3485.650744, best rearrangement setting 7
Bootstrap[24]: Time 1.203342 seconds, bootstrap likelihood -3443.431970, best rearrangement setting 8
Bootstrap[25]: Time 1.244219 seconds, bootstrap likelihood -3286.413769, best rearrangement setting 6
Bootstrap[26]: Time 1.478756 seconds, bootstrap likelihood -3370.900763, best rearrangement setting 12
Bootstrap[27]: Time 1.268625 seconds, bootstrap likelihood -2985.197250, best rearrangement setting 10
Bootstrap[28]: Time 1.453662 seconds, bootstrap likelihood -3446.754952, best rearrangement setting 11
Bootstrap[29]: Time 1.387678 seconds, bootstrap likelihood -3353.679237, best rearrangement setting 12
Bootstrap[30]: Time 1.277294 seconds, bootstrap likelihood -3268.148963, best rearrangement setting 15
Bootstrap[31]: Time 1.628477 seconds, bootstrap likelihood -3107.367628, best rearrangement setting 15
Bootstrap[32]: Time 1.414570 seconds, bootstrap likelihood -3113.508430, best rearrangement setting 6
Bootstrap[33]: Time 1.223665 seconds, bootstrap likelihood -3432.839923, best rearrangement setting 15
Bootstrap[34]: Time 1.581654 seconds, bootstrap likelihood -3502.266201, best rearrangement setting 11
Bootstrap[35]: Time 1.522324 seconds, bootstrap likelihood -3253.453056, best rearrangement setting 8
Bootstrap[36]: Time 1.262748 seconds, bootstrap likelihood -3264.461482, best rearrangement setting 9
Bootstrap[37]: Time 1.195409 seconds, bootstrap likelihood -3292.581386, best rearrangement setting 11
Bootstrap[38]: Time 1.530843 seconds, bootstrap likelihood -3372.224216, best rearrangement setting 8
Bootstrap[39]: Time 1.385764 seconds, bootstrap likelihood -3329.000280, best rearrangement setting 13
Bootstrap[40]: Time 1.461044 seconds, bootstrap likelihood -3459.597655, best rearrangement setting 13
Bootstrap[41]: Time 0.417214 seconds, bootstrap likelihood -3531.392867, best rearrangement setting 10
Bootstrap[42]: Time 1.406772 seconds, bootstrap likelihood -3440.281810, best rearrangement setting 5
Bootstrap[43]: Time 1.326578 seconds, bootstrap likelihood -3387.875791, best rearrangement setting 14
Bootstrap[44]: Time 1.295340 seconds, bootstrap likelihood -3201.577047, best rearrangement setting 10
Bootstrap[45]: Time 1.615651 seconds, bootstrap likelihood -3301.007711, best rearrangement setting 15
Bootstrap[46]: Time 1.307793 seconds, bootstrap likelihood -3407.235986, best rearrangement setting 14
Bootstrap[47]: Time 1.533467 seconds, bootstrap likelihood -3049.005355, best rearrangement setting 8
Bootstrap[48]: Time 1.689396 seconds, bootstrap likelihood -3411.800927, best rearrangement setting 6
Bootstrap[49]: Time 1.518650 seconds, bootstrap likelihood -3366.830871, best rearrangement setting 7
Bootstrap[50]: Time 1.519314 seconds, bootstrap likelihood -3549.646107, best rearrangement setting 7
Bootstrap[51]: Time 1.541124 seconds, bootstrap likelihood -3607.921931, best rearrangement setting 11
Bootstrap[52]: Time 1.706487 seconds, bootstrap likelihood -3438.679792, best rearrangement setting 12
Bootstrap[53]: Time 1.492404 seconds, bootstrap likelihood -3265.611141, best rearrangement setting 8
Bootstrap[54]: Time 1.580572 seconds, bootstrap likelihood -3251.477945, best rearrangement setting 9
Bootstrap[55]: Time 1.536842 seconds, bootstrap likelihood -3129.768493, best rearrangement setting 11
Bootstrap[56]: Time 1.288995 seconds, bootstrap likelihood -3496.533436, best rearrangement setting 5
Bootstrap[57]: Time 1.328756 seconds, bootstrap likelihood -3594.651492, best rearrangement setting 7
Bootstrap[58]: Time 1.207184 seconds, bootstrap likelihood -3444.225799, best rearrangement setting 10
Bootstrap[59]: Time 1.264831 seconds, bootstrap likelihood -3519.012306, best rearrangement setting 9
Bootstrap[60]: Time 1.384258 seconds, bootstrap likelihood -3519.420168, best rearrangement setting 7
Bootstrap[61]: Time 1.465297 seconds, bootstrap likelihood -3076.868130, best rearrangement setting 5
Bootstrap[62]: Time 1.387750 seconds, bootstrap likelihood -3229.519246, best rearrangement setting 11
Bootstrap[63]: Time 1.272152 seconds, bootstrap likelihood -3237.092001, best rearrangement setting 12
Bootstrap[64]: Time 1.522210 seconds, bootstrap likelihood -3361.641206, best rearrangement setting 7
Bootstrap[65]: Time 1.629610 seconds, bootstrap likelihood -3329.669484, best rearrangement setting 5
Bootstrap[66]: Time 1.398481 seconds, bootstrap likelihood -3345.750516, best rearrangement setting 5
Bootstrap[67]: Time 1.314576 seconds, bootstrap likelihood -3249.515792, best rearrangement setting 15
Bootstrap[68]: Time 1.360074 seconds, bootstrap likelihood -3398.325035, best rearrangement setting 11
Bootstrap[69]: Time 1.404939 seconds, bootstrap likelihood -3667.609552, best rearrangement setting 5
Bootstrap[70]: Time 1.281165 seconds, bootstrap likelihood -3033.583679, best rearrangement setting 8
Bootstrap[71]: Time 1.205416 seconds, bootstrap likelihood -3458.524013, best rearrangement setting 10
Bootstrap[72]: Time 1.628922 seconds, bootstrap likelihood -3392.468832, best rearrangement setting 11
Bootstrap[73]: Time 1.433738 seconds, bootstrap likelihood -3317.072662, best rearrangement setting 9
Bootstrap[74]: Time 1.531474 seconds, bootstrap likelihood -3095.790384, best rearrangement setting 5
Bootstrap[75]: Time 1.448179 seconds, bootstrap likelihood -3467.670763, best rearrangement setting 8
Bootstrap[76]: Time 1.140182 seconds, bootstrap likelihood -3076.268440, best rearrangement setting 9
Bootstrap[77]: Time 1.529522 seconds, bootstrap likelihood -3273.703428, best rearrangement setting 11
Bootstrap[78]: Time 1.315772 seconds, bootstrap likelihood -3510.185222, best rearrangement setting 15
Bootstrap[79]: Time 1.359448 seconds, bootstrap likelihood -3023.400556, best rearrangement setting 9
Bootstrap[80]: Time 1.535427 seconds, bootstrap likelihood -3283.354851, best rearrangement setting 15
Bootstrap[81]: Time 1.290482 seconds, bootstrap likelihood -3426.935538, best rearrangement setting 7
Bootstrap[82]: Time 1.507196 seconds, bootstrap likelihood -3126.183832, best rearrangement setting 6
Bootstrap[83]: Time 1.429196 seconds, bootstrap likelihood -3499.030146, best rearrangement setting 10
Bootstrap[84]: Time 1.561684 seconds, bootstrap likelihood -3284.090864, best rearrangement setting 11
Bootstrap[85]: Time 1.494732 seconds, bootstrap likelihood -3528.950164, best rearrangement setting 8
Bootstrap[86]: Time 1.302771 seconds, bootstrap likelihood -3464.789062, best rearrangement setting 7
Bootstrap[87]: Time 1.255981 seconds, bootstrap likelihood -3289.593935, best rearrangement setting 7
Bootstrap[88]: Time 1.315483 seconds, bootstrap likelihood -3311.361172, best rearrangement setting 12
Bootstrap[89]: Time 1.372551 seconds, bootstrap likelihood -3250.817055, best rearrangement setting 10
Bootstrap[90]: Time 1.316563 seconds, bootstrap likelihood -3599.310792, best rearrangement setting 8
Bootstrap[91]: Time 1.211454 seconds, bootstrap likelihood -3271.763478, best rearrangement setting 12
Bootstrap[92]: Time 1.438944 seconds, bootstrap likelihood -3228.332658, best rearrangement setting 13
Bootstrap[93]: Time 1.666942 seconds, bootstrap likelihood -3396.189039, best rearrangement setting 15
Bootstrap[94]: Time 1.324722 seconds, bootstrap likelihood -3621.354535, best rearrangement setting 5
Bootstrap[95]: Time 1.259668 seconds, bootstrap likelihood -3482.040581, best rearrangement setting 5
Bootstrap[96]: Time 1.814558 seconds, bootstrap likelihood -3389.285711, best rearrangement setting 13
Bootstrap[97]: Time 1.597387 seconds, bootstrap likelihood -3251.650413, best rearrangement setting 11
Bootstrap[98]: Time 1.412277 seconds, bootstrap likelihood -3082.388144, best rearrangement setting 6
Bootstrap[99]: Time 1.235482 seconds, bootstrap likelihood -3024.665769, best rearrangement setting 14


Overall Time for 100 Rapid Bootstraps 156.437182 seconds
Average Time per Rapid Bootstrap 1.564372 seconds

Starting ML Search ...


Printed linked AA GTR matrix that achieved an overall improvement of 183.442104 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 14.381597 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.619230 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.172234 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.056117 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided

Fast ML optimization finished

Fast ML search Time: 96.656056 seconds


Printed linked AA GTR matrix that achieved an overall improvement of 179.127060 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 13.603182 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.559716 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.218731 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.051378 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided

Slow ML Search 0 Likelihood: -3381.313322
Slow ML Search 1 Likelihood: -3381.564894
Slow ML Search 2 Likelihood: -3381.564894
Slow ML Search 3 Likelihood: -3381.564895
Slow ML Search 4 Likelihood: -3381.565002
Slow ML Search 5 Likelihood: -3381.565016
Slow ML Search 6 Likelihood: -3381.564894
Slow ML Search 7 Likelihood: -3381.564894
Slow ML Search 8 Likelihood: -3381.569367
Slow ML Search 9 Likelihood: -3381.552210
Slow ML optimization finished

Slow ML search Time: 65.934007 seconds

Printed linked AA GTR matrix that achieved an overall improvement of 179.127261 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 13.603085 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.559575 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.218726 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.051380 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-nad1a.renamed.muscle.Oligohymenophorea_Partition_No Name Provided

Thorough ML search Time: 29.196523 seconds

Final ML Optimization Likelihood: -3381.313134

Model Information:

Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA
alpha: 0.254727
Tree-Length: 7.762888
rate A <-> R: 0.000000
rate A <-> N: 0.000000
rate A <-> D: 0.000000
rate A <-> C: 7.628963
rate A <-> Q: 0.000000
rate A <-> E: 0.000000
rate A <-> G: 0.000000
rate A <-> H: 0.000000
rate A <-> I: 0.000000
rate A <-> L: 0.000000
rate A <-> K: 0.000000
rate A <-> M: 3.720272
rate A <-> F: 0.997605
rate A <-> P: 0.000000
rate A <-> S: 11.149029
rate A <-> T: 11.178429
rate A <-> W: 0.000000
rate A <-> Y: 0.000000
rate A <-> V: 9.229458
rate R <-> N: 0.000000
rate R <-> D: 0.000000
rate R <-> C: 0.000000
rate R <-> Q: 8.931949
rate R <-> E: 4.721487
rate R <-> G: 0.000000
rate R <-> H: 20.145324
rate R <-> I: 0.000000
rate R <-> L: 0.089460
rate R <-> K: 12.173354
rate R <-> M: 0.000000
rate R <-> F: 0.986818
rate R <-> P: 6.592212
rate R <-> S: 0.000000
rate R <-> T: 0.000000
rate R <-> W: 0.000000
rate R <-> Y: 0.000000
rate R <-> V: 0.000000
rate N <-> D: 21.779450
rate N <-> C: 0.000000
rate N <-> Q: 0.325448
rate N <-> E: 2.856165
rate N <-> G: 0.452384
rate N <-> H: 42.721987
rate N <-> I: 1.085047
rate N <-> L: 0.901205
rate N <-> K: 8.166907
rate N <-> M: 0.000000
rate N <-> F: 0.568481
rate N <-> P: 3.678195
rate N <-> S: 19.519548
rate N <-> T: 1.877260
rate N <-> W: 0.000000
rate N <-> Y: 0.967913
rate N <-> V: 0.000000
rate D <-> C: 0.000000
rate D <-> Q: 0.000000
rate D <-> E: 25.426850
rate D <-> G: 8.754491
rate D <-> H: 0.000000
rate D <-> I: 0.000000
rate D <-> L: 0.000000
rate D <-> K: 0.000000
rate D <-> M: 0.000000
rate D <-> F: 0.000000
rate D <-> P: 0.000000
rate D <-> S: 2.372886
rate D <-> T: 0.000000
rate D <-> W: 0.000000
rate D <-> Y: 3.073788
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: 0.548137
rate C <-> L: 0.810756
rate C <-> K: 0.000000
rate C <-> M: 9.646197
rate C <-> F: 2.365149
rate C <-> P: 13.807522
rate C <-> S: 11.611904
rate C <-> T: 0.000000
rate C <-> W: 0.000000
rate C <-> Y: 8.843193
rate C <-> V: 0.000000
rate Q <-> E: 7.032141
rate Q <-> G: 0.000000
rate Q <-> H: 100.159833
rate Q <-> I: 0.000000
rate Q <-> L: 0.000000
rate Q <-> K: 0.000000
rate Q <-> M: 0.000000
rate Q <-> F: 0.000000
rate Q <-> P: 0.000000
rate Q <-> S: 10.323950
rate Q <-> T: 0.000000
rate Q <-> W: 0.000000
rate Q <-> Y: 5.386931
rate Q <-> V: 0.000000
rate E <-> G: 2.283717
rate E <-> H: 0.000000
rate E <-> I: 0.000000
rate E <-> L: 0.000000
rate E <-> K: 0.000000
rate E <-> M: 0.000000
rate E <-> F: 0.000000
rate E <-> P: 0.000000
rate E <-> S: 0.928899
rate E <-> T: 0.000000
rate E <-> W: 0.000000
rate E <-> Y: 0.000000
rate E <-> V: 0.000000
rate G <-> H: 0.000000
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: 7.653223
rate G <-> T: 0.000000
rate G <-> W: 3.331431
rate G <-> Y: 0.000000
rate G <-> V: 0.132840
rate H <-> I: 0.000000
rate H <-> L: 0.000000
rate H <-> K: 15.505568
rate H <-> M: 0.000000
rate H <-> F: 0.000000
rate H <-> P: 0.000000
rate H <-> S: 11.781691
rate H <-> T: 0.000000
rate H <-> W: 0.000000
rate H <-> Y: 44.820029
rate H <-> V: 0.000000
rate I <-> L: 12.950551
rate I <-> K: 2.653836
rate I <-> M: 29.973073
rate I <-> F: 4.481090
rate I <-> P: 0.000000
rate I <-> S: 2.022686
rate I <-> T: 0.000000
rate I <-> W: 0.000000
rate I <-> Y: 1.524267
rate I <-> V: 60.981170
rate L <-> K: 0.000000
rate L <-> M: 8.823297
rate L <-> F: 6.901489
rate L <-> P: 1.589318
rate L <-> S: 0.000000
rate L <-> T: 2.209061
rate L <-> W: 2.648305
rate L <-> Y: 1.577436
rate L <-> V: 2.284972
rate K <-> M: 3.781632
rate K <-> F: 1.962384
rate K <-> P: 0.000000
rate K <-> S: 4.288278
rate K <-> T: 0.000000
rate K <-> W: 0.000000
rate K <-> Y: 0.000000
rate K <-> V: 0.000000
rate M <-> F: 0.000000
rate M <-> P: 0.000000
rate M <-> S: 0.000000
rate M <-> T: 0.000000
rate M <-> W: 0.000000
rate M <-> Y: 0.000000
rate M <-> V: 0.578265
rate F <-> P: 4.450551
rate F <-> S: 2.519784
rate F <-> T: 0.000000
rate F <-> W: 5.870632
rate F <-> Y: 8.258650
rate F <-> V: 0.444989
rate P <-> S: 4.324076
rate P <-> T: 0.000000
rate P <-> W: 0.000000
rate P <-> Y: 2.335714
rate P <-> V: 2.385606
rate S <-> T: 23.141262
rate S <-> W: 0.000000
rate S <-> Y: 0.358492
rate S <-> V: 0.000000
rate T <-> W: 0.000000
rate T <-> Y: 0.000000
rate T <-> V: 27.527163
rate W <-> Y: 0.000000
rate W <-> V: 0.000000
rate Y <-> V: 1.000000

freq pi(A): 0.056721
freq pi(R): 0.020507
freq pi(N): 0.040730
freq pi(D): 0.013264
freq pi(C): 0.015710
freq pi(Q): 0.014393
freq pi(E): 0.041201
freq pi(G): 0.060389
freq pi(H): 0.006116
freq pi(I): 0.079483
freq pi(L): 0.162351
freq pi(K): 0.031794
freq pi(M): 0.023423
freq pi(F): 0.146173
freq pi(P): 0.024270
freq pi(S): 0.078073
freq pi(T): 0.032171
freq pi(W): 0.015240
freq pi(Y): 0.059166
freq pi(V): 0.078825


ML search took 191.918038 secs or 0.053311 hours

Combined Bootstrap and ML search took 348.356125 secs or 0.096766 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-nad1a.renamed.muscle.Oligohymenophorea



Found 1 tree in File /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_bestTree.RAxML-PROTGAMMAGTR-nad1a.renamed.muscle.Oligohymenophorea

Program execution info written to /N/dc2/projects/marinovg/Paramecium/variation/2015-09-07-assemblies/mito/supermatrix/RAxML_info.RAxML-PROTGAMMAGTR-nad1a.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-nad1a.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-nad1a.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-nad1a.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-nad1a.renamed.muscle.Oligohymenophorea

Overall execution time for full ML analysis: 348.372292 secs or 0.096770 hours or 0.004032 days