IMPORTANT WARNING: Alignment column 34 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 39 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 52 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 71 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 72 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 123 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 124 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 125 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 204 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 205 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 206 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 208 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 209 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 210 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 211 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 212 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 213 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 214 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 215 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 216 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 217 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 256 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 257 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 258 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 259 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 260 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 261 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 275 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 276 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 277 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 278 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 295 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 328 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 335 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 342 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 343 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 375 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 390 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 519 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 534 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 610 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 611 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 612 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 613 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 614 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 615 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 658 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 659 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 735 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 746 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 760 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 806 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 840 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 875 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 885 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 57 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_M2772_77x900_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 575 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.305281 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): 0.271404 pi(C): 0.209156 pi(G): 0.230331 pi(T): 0.289109 1.194615 -7269.316672 3.234402 -7258.830390 7.958942 -7257.408579 15.615051 -7220.188959 21.917365 -7205.503459 29.296147 -7202.872927 38.739212 -7202.046031 48.702758 -7201.724849 58.866904 -7201.628390 68.033219 -7201.628390 75.848284 -7194.039243 Overall Time for 1 Inference 75.921219 Likelihood : -7194.039243 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2772_77x900_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2772_77x900_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2772_77x900_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2772_77x900_2006.phy_RAXML