IMPORTANT WARNING: Alignment column 34 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 853 contains only undetermined values which will be treated as missing data

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 
undetermined columns removed is printed to file /auto/dufayard/res/ori_nucl_raxml/nucleic_M2856_61x970_2006.phy.reduced


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

Alignment has 686 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.081612

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): 0.243352 pi(C): 0.264791 pi(G): 0.271342 pi(T): 0.220515



1.942663 -25356.891123
3.882779 -25333.116663
10.662509 -25207.064416
19.082174 -25182.510069
29.945344 -25169.490933
40.563143 -25166.841191
51.481673 -25165.588861
63.348491 -25164.419141
74.404904 -25163.553964
85.176448 -25163.223333
87.910472 -25163.223333
100.460691 -25118.383728


Overall Time for 1 Inference 100.476431
Likelihood   : -25118.383728


Parsimony starting tree written to:    /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2856_61x970_2006.phy_RAXML
Final tree written to:                 /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2856_61x970_2006.phy_RAXML
Execution Log File written to:         /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2856_61x970_2006.phy_RAXML
Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2856_61x970_2006.phy_RAXML