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 89 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.87%

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: 89
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/HOG332.muscle -n HOG332.muscle -m PROTCATGTR -T 16 -p 12345 


Partition: 0 with name: No Name Provided
Base frequencies: 0.030 0.036 0.078 0.057 0.007 0.152 0.102 0.031 0.026 0.068 0.071 0.112 0.018 0.039 0.020 0.078 0.019 0.006 0.018 0.032 


Printed linked AA GTR matrix that achieved an overall improvement of 187.393957 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.HOG332.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 34.408652 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.HOG332.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 7.496411 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.HOG332.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.051654 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.HOG332.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.483616 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.HOG332.muscle_Partition_No Name Provided

Inference[0]: Time 3.383982 CAT-based likelihood -1228.665141, best rearrangement setting 1
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 72.659867 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.HOG332.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 9.710045 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.HOG332.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 1.876405 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.HOG332.muscle_Partition_No Name Provided


Printed linked AA GTR matrix that achieved an overall improvement of 0.087603 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.HOG332.muscle_Partition_No Name Provided

Inference[0] final GAMMA-based Likelihood: -1373.406733 tree written to file /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_result.HOG332.muscle


Starting final GAMMA-based thorough Optimization on tree 0 likelihood -1373.406733 .... 

Final GAMMA-based Score of best tree -1373.406733

Program execution info written to /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_info.HOG332.muscle
Best-scoring ML tree written to: /N/dc2/projects/marinovg/2015-04-22-TFs/OMA-leq1e-4-fix/Output/HOGFasta/RAxML/RAxML_bestTree.HOG332.muscle

Overall execution time: 6.368895 secs or 0.001769 hours or 0.000074 days