IMPORTANT WARNING: Alignment column 347 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 760 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 970 contains only undetermined values which will be treated as missing data


IMPORTANT WARNING: Sequences tax2 and tax3 are exactly identical

IMPORTANT WARNING
Found 1 sequence that is 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_M2901_56x1802_2006.phy.reduced


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

Alignment has 642 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.305960

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): 0.265601 pi(C): 0.204059 pi(G): 0.259248 pi(T): 0.271092



0.883245 -7935.128599
2.536703 -7892.407718
6.659656 -7890.322320
12.866481 -7862.586265
20.315171 -7850.594868
30.246452 -7848.185185
38.987844 -7847.562585
46.308829 -7846.480317
54.106132 -7845.873966
62.402114 -7845.780959
66.136803 -7845.780959
73.382987 -7828.921722


Overall Time for 1 Inference 73.399197
Likelihood   : -7828.921722


Parsimony starting tree written to:    /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2901_56x1802_2006.phy_RAXML
Final tree written to:                 /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2901_56x1802_2006.phy_RAXML
Execution Log File written to:         /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2901_56x1802_2006.phy_RAXML
Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2901_56x1802_2006.phy_RAXML