IMPORTANT WARNING: Alignment column 1 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 207 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 262 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 447 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 448 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 461 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 667 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 7 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_M2786_104x1051_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 717 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.351881 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): 0.226094 pi(C): 0.270569 pi(G): 0.292067 pi(T): 0.211270 3.639810 -15761.450606 7.280077 -15751.401007 21.395045 -15686.599627 35.252854 -15677.687977 50.015840 -15674.720145 64.124606 -15674.266682 77.890070 -15673.832495 91.857787 -15673.588353 111.768670 -15673.505119 131.451752 -15673.382285 160.726737 -15673.298750 181.369032 -15673.298750 196.674827 -15658.378488 Overall Time for 1 Inference 196.691837 Likelihood : -15658.378488 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2786_104x1051_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2786_104x1051_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2786_104x1051_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2786_104x1051_2006.phy_RAXML