IMPORTANT WARNING: Alignment column 1122 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1123 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1175 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1286 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 1287 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 5 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_M2932_68x1712_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 1264 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.567482 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): 0.232862 pi(C): 0.231365 pi(G): 0.303269 pi(T): 0.232503 4.128665 -15002.275705 7.714531 -14994.903056 16.197933 -14994.902361 32.659522 -14952.643061 50.445967 -14941.350500 64.451255 -14937.920353 80.666245 -14935.009535 99.922291 -14934.663835 122.305744 -14934.562941 137.177405 -14934.562941 153.718276 -14923.182906 Overall Time for 1 Inference 153.734296 Likelihood : -14923.182906 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2932_68x1712_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2932_68x1712_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2932_68x1712_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2932_68x1712_2006.phy_RAXML