IMPORTANT WARNING: Alignment column 185 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 276 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 543 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 591 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 1135 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Sequences tax55 and tax56 are exactly identical IMPORTANT WARNING Found 1 sequence that is exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. 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 sequence duplicates and undetermined columns removed is printed to file /auto/dufayard/res/ori_nucl_raxml/nucleic_M2662_60x1348_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 664 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.217569 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): 0.256079 pi(C): 0.224855 pi(G): 0.301653 pi(T): 0.217412 1.615643 -12480.163749 3.414003 -12480.163749 9.081164 -12422.542995 16.402563 -12379.898838 25.859349 -12376.457942 35.439406 -12374.190867 44.702651 -12372.944676 53.821183 -12372.744663 64.957970 -12372.373440 74.877847 -12372.283360 83.326079 -12372.100838 84.207945 -12372.100838 94.046083 -12346.451523 Overall Time for 1 Inference 94.062058 Likelihood : -12346.451523 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2662_60x1348_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2662_60x1348_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2662_60x1348_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2662_60x1348_2006.phy_RAXML