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 174 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 27.88%

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: 174
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/HOG123.muscle -n HOG123.muscle -m PROTCATGTR -T 16 -p 12345 


Partition: 0 with name: No Name Provided
Base frequencies: 0.025 0.025 0.089 0.040 0.011 0.095 0.087 0.025 0.019 0.069 0.083 0.099 0.031 0.065 0.027 0.070 0.048 0.004 0.044 0.046 


Printed linked AA GTR matrix that achieved an overall improvement of 337.440536 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.HOG123.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 178.231562 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.HOG123.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 48.002285 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.HOG123.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 4.312563 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.HOG123.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.568307 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.HOG123.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.591411 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.HOG123.muscle_Partition_No Name Provided

Inference[0]: Time 25.265808 CAT-based likelihood -2053.107962, 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 165.003641 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.HOG123.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 14.746298 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.HOG123.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 3.629717 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.HOG123.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.625664 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.HOG123.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.129396 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.HOG123.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.063056 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.HOG123.muscle_Partition_No Name Provided

Inference[0] final GAMMA-based Likelihood: -2348.671489 tree written to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_result.HOG123.muscle


Starting final GAMMA-based thorough Optimization on tree 0 likelihood -2348.671489 .... 

Final GAMMA-based Score of best tree -2348.671489

Program execution info written to /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_info.HOG123.muscle
Best-scoring ML tree written to: /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_bestTree.HOG123.muscle

Overall execution time: 47.263687 secs or 0.013129 hours or 0.000547 days