IMPORTANT WARNING: Alignment column 206 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 207 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 690 contains only undetermined values which will be treated as missing data


IMPORTANT WARNING: Sequences tax39 and tax45 are exactly identical


IMPORTANT WARNING: Sequences tax50 and tax82 are exactly identical


IMPORTANT WARNING: Sequences tax50 and tax83 are exactly identical


IMPORTANT WARNING: Sequences tax80 and tax85 are exactly identical

IMPORTANT WARNING
Found 4 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.


IMPORTANT WARNING
Found 3 columns that contain only undetermined values which will be treated as missing data.
Normally these columns should be excluded from the analysis.

Just in case you might need it, an alignment file with 
sequence duplicates and undetermined columns removed is printed to file /auto/dufayard/res/ori_nucl_raxml/nucleic_M2933_99x1634_2006.phy.reduced


You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008

Alignment has 578 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.615519

RAxML rapid hill-climbing mode

Executing 1 inference on the original alignment using a distinct randomized MP tree

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
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
Empirical Base Frequencies:
pi(A): 0.216029 pi(C): 0.264051 pi(G): 0.257874 pi(T): 0.262047



3.190977 -7694.304229
5.816716 -7678.835980
13.047578 -7678.817304
23.795384 -7678.817304
39.400430 -7659.277551
50.598252 -7648.310081
63.380499 -7639.470981
75.142779 -7632.242877
82.584122 -7631.849626
88.016175 -7631.757376
102.061335 -7631.290222
111.913376 -7631.205396
123.559313 -7631.123545
140.780854 -7631.044530
154.217074 -7631.044530
165.362085 -7620.232020


Overall Time for 1 Inference 165.503945
Likelihood   : -7620.232020


Parsimony starting tree written to:    /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2933_99x1634_2006.phy_RAXML
Final tree written to:                 /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2933_99x1634_2006.phy_RAXML
Execution Log File written to:         /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2933_99x1634_2006.phy_RAXML
Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2933_99x1634_2006.phy_RAXML