IMPORTANT WARNING: Alignment column 159 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 338 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 392 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 393 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 434 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 463 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 6 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_M2588_68x1196_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 730 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.213998 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): 0.288367 pi(C): 0.251646 pi(G): 0.173559 pi(T): 0.286428 2.746218 -12258.304348 4.802018 -12254.707698 9.409075 -12254.707666 17.573240 -12135.370260 29.103414 -12102.595614 36.183478 -12098.125021 44.647358 -12096.324972 53.817124 -12095.460206 64.744240 -12095.142989 74.311706 -12095.142989 96.059166 -12023.711430 Overall Time for 1 Inference 96.075382 Likelihood : -12023.711430 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2588_68x1196_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2588_68x1196_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2588_68x1196_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2588_68x1196_2006.phy_RAXML