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 488 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 27.24%

RAxML rapid hill-climbing mode

Using 1 distinct models/data partitions with joint branch length optimization


Executing 1 inferences on the original alignment using 1 distinct randomized MP trees

All free model parameters will be estimated by RAxML
ML estimate of 25 per site rate categories

Likelihood of final tree will be evaluated and optimized under GAMMA

GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units

Partition: 0
Alignment Patterns: 488
Name: No Name Provided
DataType: AA
Substitution Matrix: GTR
Using empirical base frequencies




RAxML was called as follows:

raxml -s /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/muscle/HOG33.muscle -n HOG33.muscle -m PROTCATGTR -T 16 -p 12345 


Partition: 0 with name: No Name Provided
Base frequencies: 0.032 0.061 0.063 0.067 0.018 0.066 0.107 0.039 0.019 0.069 0.100 0.111 0.025 0.048 0.029 0.042 0.030 0.005 0.034 0.034 


Printed linked AA GTR matrix that achieved an overall improvement of 215.210115 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 485.250557 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 93.517478 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 35.675022 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 4.019334 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.553398 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.796149 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided

Inference[0]: Time 21.445649 CAT-based likelihood -5670.255300, best rearrangement setting 5
alpha[0]: 1.000000 


Conducting final model optimizations on all 1 trees under GAMMA-based models ....


Printed linked AA GTR matrix that achieved an overall improvement of 182.013316 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 15.731864 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.052002 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.177549 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.056581 log likelihood units for partition No Name Provided to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_proteinGTRmodel.HOG33.muscle_Partition_No Name Provided

Inference[0] final GAMMA-based Likelihood: -6205.398371 tree written to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_result.HOG33.muscle


Starting final GAMMA-based thorough Optimization on tree 0 likelihood -6205.398371 .... 

Final GAMMA-based Score of best tree -6205.398371

Program execution info written to /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_info.HOG33.muscle
Best-scoring ML tree written to: /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_bestTree.HOG33.muscle

Overall execution time: 39.306219 secs or 0.010918 hours or 0.000455 days