IMPORTANT WARNING: Alignment column 722 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 723 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 724 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 725 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 726 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 727 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 728 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 729 contains only undetermined values which will be treated as missing data
IMPORTANT WARNING: Alignment column 730 contains only undetermined values which will be treated as missing data


IMPORTANT WARNING: Sequences tax2 and tax66 are exactly identical


IMPORTANT WARNING: Sequences tax3 and tax5 are exactly identical


IMPORTANT WARNING: Sequences tax10 and tax11 are exactly identical


IMPORTANT WARNING: Sequences tax10 and tax12 are exactly identical


IMPORTANT WARNING: Sequences tax10 and tax13 are exactly identical


IMPORTANT WARNING: Sequences tax10 and tax14 are exactly identical


IMPORTANT WARNING: Sequences tax21 and tax22 are exactly identical


IMPORTANT WARNING: Sequences tax33 and tax35 are exactly identical


IMPORTANT WARNING: Sequences tax36 and tax37 are exactly identical


IMPORTANT WARNING: Sequences tax36 and tax38 are exactly identical


IMPORTANT WARNING: Sequences tax45 and tax46 are exactly identical


IMPORTANT WARNING: Sequences tax47 and tax48 are exactly identical


IMPORTANT WARNING: Sequences tax55 and tax56 are exactly identical


IMPORTANT WARNING: Sequences tax55 and tax58 are exactly identical


IMPORTANT WARNING: Sequences tax62 and tax63 are exactly identical

IMPORTANT WARNING
Found 15 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.


IMPORTANT WARNING
Found 9 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_M2661_66x1027_2006.phy.reduced


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

Alignment has 596 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.212520

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): 0.221893 pi(C): 0.308485 pi(G): 0.227064 pi(T): 0.242558



1.379809 -9195.417275
3.017635 -9195.417263
8.798010 -9169.308461
12.486363 -9153.389688
17.109526 -9150.544955
23.628091 -9149.514319
33.729736 -9149.188955
41.162898 -9149.091283
45.082909 -9149.091283
54.491582 -9131.948216


Overall Time for 1 Inference 54.507883
Likelihood   : -9131.948216


Parsimony starting tree written to:    /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2661_66x1027_2006.phy_RAXML
Final tree written to:                 /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2661_66x1027_2006.phy_RAXML
Execution Log File written to:         /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2661_66x1027_2006.phy_RAXML
Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2661_66x1027_2006.phy_RAXML