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 351 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 20.69%

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: 351
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/HOG67.muscle -n HOG67.muscle -m PROTCATGTR -T 16 -p 12345 


Partition: 0 with name: No Name Provided
Base frequencies: 0.022 0.031 0.080 0.058 0.009 0.133 0.086 0.039 0.017 0.071 0.071 0.098 0.020 0.043 0.052 0.059 0.032 0.002 0.036 0.039 


Printed linked AA GTR matrix that achieved an overall improvement of 565.691867 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.HOG67.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 206.270456 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.HOG67.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 40.052301 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.HOG67.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 2.554915 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.HOG67.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.700894 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.HOG67.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.240342 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.HOG67.muscle_Partition_No Name Provided

Inference[0]: Time 9.616213 CAT-based likelihood -4708.870132, 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 159.131100 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.HOG67.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 10.773179 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.HOG67.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.778194 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.HOG67.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.157359 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.HOG67.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.041538 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.HOG67.muscle_Partition_No Name Provided

Inference[0] final GAMMA-based Likelihood: -5229.895363 tree written to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_result.HOG67.muscle


Starting final GAMMA-based thorough Optimization on tree 0 likelihood -5229.895363 .... 

Final GAMMA-based Score of best tree -5229.780460

Program execution info written to /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_info.HOG67.muscle
Best-scoring ML tree written to: /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_bestTree.HOG67.muscle

Overall execution time: 18.950732 secs or 0.005264 hours or 0.000219 days