IMPORTANT WARNING: Alignment column 117 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 935 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 986 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 1427 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 1795 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 1859 contains only undetermined values which will be treated as missing data


IMPORTANT WARNING: Sequences tax17 and tax19 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 6 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_M2565_51x1951_2006.phy.reduced


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

Alignment has 763 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.038492

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): 0.262891 pi(C): 0.218394 pi(G): 0.281026 pi(T): 0.237690



1.329619 -14819.621371
3.043435 -14801.604830
7.846943 -14731.323470
14.629839 -14694.706499
21.450019 -14691.468550
28.121821 -14690.100202
35.732411 -14689.776763
43.943310 -14689.677570
51.030305 -14689.582396
52.948567 -14689.582396
61.545096 -14657.959001


Overall Time for 1 Inference 61.560527
Likelihood   : -14657.959001


Parsimony starting tree written to:    /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2565_51x1951_2006.phy_RAXML
Final tree written to:                 /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2565_51x1951_2006.phy_RAXML
Execution Log File written to:         /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2565_51x1951_2006.phy_RAXML
Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2565_51x1951_2006.phy_RAXML