IMPORTANT WARNING: Alignment column 749 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Sequences tax51 and tax52 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 1 column that contains 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_M2921_54x966_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 397 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.072310 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): 0.247651 pi(C): 0.221473 pi(G): 0.316389 pi(T): 0.214487 0.617944 -6550.528562 1.616559 -6523.721995 3.840844 -6523.721995 7.002970 -6488.604030 10.275391 -6472.971814 15.609103 -6469.199160 20.669081 -6468.249740 25.699208 -6468.148868 30.713844 -6468.057325 35.195094 -6467.517998 39.587019 -6466.764096 42.136486 -6466.764096 46.795126 -6438.973412 Overall Time for 1 Inference 46.811104 Likelihood : -6438.973412 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2921_54x966_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2921_54x966_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2921_54x966_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2921_54x966_2006.phy_RAXML