IMPORTANT WARNING: Alignment column 27 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 67 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 143 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 150 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 319 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 500 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 555 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 559 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 581 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 615 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 1033 contains only undetermined values which will be treated as missing data


IMPORTANT WARNING: Sequences tax17 and tax19 are exactly identical


IMPORTANT WARNING: Sequences tax30 and tax50 are exactly identical


IMPORTANT WARNING: Sequences tax52 and tax53 are exactly identical


IMPORTANT WARNING: Sequences tax57 and tax58 are exactly identical


IMPORTANT WARNING: Sequences tax61 and tax74 are exactly identical


IMPORTANT WARNING: Sequences tax65 and tax66 are exactly identical


IMPORTANT WARNING: Sequences tax84 and tax85 are exactly identical


IMPORTANT WARNING: Sequences tax90 and tax91 are exactly identical


IMPORTANT WARNING: Sequences tax102 and tax103 are exactly identical


IMPORTANT WARNING: Sequences tax102 and tax106 are exactly identical

IMPORTANT WARNING
Found 10 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.


IMPORTANT WARNING
Found 11 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_M2752_106x1292_2006.phy.reduced


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

Alignment has 427 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.066388

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): 0.306007 pi(C): 0.184092 pi(G): 0.157798 pi(T): 0.352104



1.503306 -7916.178392
3.596025 -7899.125027
9.763496 -7889.503140
15.929972 -7876.923072
21.999168 -7874.840461
25.961376 -7874.278790
33.682189 -7874.065763
41.708968 -7873.971721
52.799521 -7873.758844
63.128301 -7873.758844
69.911472 -7869.188264


Overall Time for 1 Inference 69.928858
Likelihood   : -7869.188264


Parsimony starting tree written to:    /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2752_106x1292_2006.phy_RAXML
Final tree written to:                 /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2752_106x1292_2006.phy_RAXML
Execution Log File written to:         /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2752_106x1292_2006.phy_RAXML
Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2752_106x1292_2006.phy_RAXML