This is RAxML version 7.2.8 released by Alexandros Stamatakis in October 2010.

With greatly appreciated code contributions by:
Andre Aberer (TUM)
Simon Berger (TUM)
John Cazes (TACC)
Michael Ott (TUM)
Nick Pattengale (UNM)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (Univ. Tsukuba)


Alignment has 8854 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 89.68%

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 user-specifed trees

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: 8854
Name: No Name Provided
DataType: AA
Substitution Matrix: WAG
Fixed Base Frequencies:




RAxML was called as follows:

raxmlHPC -T 12 -s pplacer_ref211.msa.phylip -n PolB_Refs20191224_linsi -m PROTGAMMAWAG -g pplacer_ref211.msa.midpoint.ETE3.nwk 


Testing which likelihood implementation to use
Standard Implementation full tree traversal time: 0.963861
Subtree Equality Vectors for gap columns full tree traversal time: 0.262621
... using SEV-based implementation

Inference[0]: Time 37.293066 GAMMA-based likelihood -446015.217671, best rearrangement setting 5
alpha[0]: 1.417299 


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

Inference[0] final GAMMA-based Likelihood: -446015.215646 tree written to file /lustre/aptmp/endo/Tara/TOPCv4/Pplacer_reference_tree/RAxML_result.PolB_Refs20191224_linsi


Starting final GAMMA-based thorough Optimization on tree 0 likelihood -446015.215646 .... 

Final GAMMA-based Score of best tree -446015.215646

Program execution info written to /lustre/aptmp/endo/Tara/TOPCv4/Pplacer_reference_tree/RAxML_info.PolB_Refs20191224_linsi
Best-scoring ML tree written to: /lustre/aptmp/endo/Tara/TOPCv4/Pplacer_reference_tree/RAxML_bestTree.PolB_Refs20191224_linsi

Overall execution time: 40.095830 secs or 0.011138 hours or 0.000464 days