
RAxML can't, parse the alignment file as phylip file 
it will now try to parse it as FASTA file


This is the RAxML Master Pthread

This is RAxML Worker Pthread Number: 1


This is RAxML version 7.7.6 released by Alexandros Stamatakis on August 29 2013.

With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)


Alignment has 313 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.00%

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: 313
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR




RAxML was called as follows:

raxml -s example_data/HA_alignment.fasta -n HA_alignment -m GTRCAT -p1 -T 2 


Partition: 0 with name: No Name Provided
Base frequencies: 0.345 0.188 0.227 0.239 

Inference[0]: Time 0.756005 CAT-based likelihood -5217.371828, best rearrangement setting 5


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

Inference[0] final GAMMA-based Likelihood: -6064.728910 tree written to file /Users/sarah/Desktop/phydms/tutorial/RAxML_result.HA_alignment


Starting final GAMMA-based thorough Optimization on tree 0 likelihood -6064.728910 .... 

Final GAMMA-based Score of best tree -6064.728910

Program execution info written to /Users/sarah/Desktop/phydms/tutorial/RAxML_info.HA_alignment
Best-scoring ML tree written to: /Users/sarah/Desktop/phydms/tutorial/RAxML_bestTree.HA_alignment

Overall execution time: 1.823443 secs or 0.000507 hours or 0.000021 days

