IMPORTANT WARNING: Alignment column 189 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 477 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 602 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 603 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 604 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 605 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 606 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 607 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 608 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 609 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 610 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 611 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 612 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 613 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 614 contains only undetermined values which will be treated as missing data


IMPORTANT WARNING: Sequences tax6 and tax8 are exactly identical


IMPORTANT WARNING: Sequences tax11 and tax12 are exactly identical


IMPORTANT WARNING: Sequences tax15 and tax16 are exactly identical


IMPORTANT WARNING: Sequences tax15 and tax17 are exactly identical


IMPORTANT WARNING: Sequences tax31 and tax32 are exactly identical


IMPORTANT WARNING: Sequences tax40 and tax41 are exactly identical


IMPORTANT WARNING: Sequences tax54 and tax59 are exactly identical


IMPORTANT WARNING: Sequences tax70 and tax71 are exactly identical


IMPORTANT WARNING: Sequences tax70 and tax73 are exactly identical

IMPORTANT WARNING
Found 9 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.


IMPORTANT WARNING
Found 15 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_M2708_78x1107_2006.phy.reduced


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

Alignment has 616 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.413858

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): 0.239818 pi(C): 0.285520 pi(G): 0.239029 pi(T): 0.235633



1.935916 -6588.521580
4.074175 -6579.602432
10.181263 -6579.342494
19.933046 -6552.480910
28.818852 -6545.528802
35.675222 -6544.172319
45.559465 -6543.828962
58.196092 -6543.729131
75.187125 -6543.635515
79.824354 -6543.635515
90.299765 -6527.915177


Overall Time for 1 Inference 90.316264
Likelihood   : -6527.915177


Parsimony starting tree written to:    /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2708_78x1107_2006.phy_RAXML
Final tree written to:                 /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2708_78x1107_2006.phy_RAXML
Execution Log File written to:         /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2708_78x1107_2006.phy_RAXML
Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2708_78x1107_2006.phy_RAXML