IMPORTANT WARNING: Alignment column 125 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 242 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 346 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_M2764_57x803_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 628 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.234559 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): 0.241139 pi(C): 0.288800 pi(G): 0.277323 pi(T): 0.192738 1.176418 -10205.088518 2.828076 -10198.150304 7.607034 -10177.645101 13.787206 -10169.546985 21.829794 -10167.531498 29.815750 -10166.473236 39.097782 -10166.257518 46.735011 -10166.122037 54.326363 -10166.028951 55.743442 -10166.028951 62.429623 -10157.642201 Overall Time for 1 Inference 62.445238 Likelihood : -10157.642201 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2764_57x803_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2764_57x803_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2764_57x803_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2764_57x803_2006.phy_RAXML