IMPORTANT WARNING: Alignment column 588 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 589 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 590 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 592 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 593 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 594 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 595 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 596 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 597 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 598 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 599 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 600 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 980 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 994 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 995 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 996 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 997 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Sequences tax24 and tax25 are exactly identical IMPORTANT WARNING: Sequences tax39 and tax40 are exactly identical IMPORTANT WARNING: Sequences tax44 and tax45 are exactly identical IMPORTANT WARNING: Sequences tax50 and tax52 are exactly identical IMPORTANT WARNING: Sequences tax50 and tax53 are exactly identical IMPORTANT WARNING: Sequences tax54 and tax55 are exactly identical IMPORTANT WARNING: Sequences tax54 and tax58 are exactly identical IMPORTANT WARNING: Sequences tax54 and tax60 are exactly identical IMPORTANT WARNING: Sequences tax54 and tax62 are exactly identical IMPORTANT WARNING: Sequences tax70 and tax76 are exactly identical IMPORTANT WARNING: Sequences tax70 and tax77 are exactly identical IMPORTANT WARNING: Sequences tax71 and tax74 are exactly identical IMPORTANT WARNING: Sequences tax80 and tax81 are exactly identical IMPORTANT WARNING Found 13 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. IMPORTANT WARNING Found 18 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_M2711_123x1181_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 617 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.187818 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): 0.222214 pi(C): 0.334190 pi(G): 0.223339 pi(T): 0.220257 2.822772 -10752.216777 6.282468 -10737.381691 17.486844 -10737.381686 38.736771 -10706.318506 44.322894 -10694.497075 66.120662 -10683.196930 81.182770 -10681.903468 100.913625 -10681.443253 130.740468 -10681.245179 148.556803 -10681.245179 170.735782 -10655.801038 Overall Time for 1 Inference 170.754392 Likelihood : -10655.801038 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2711_123x1181_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2711_123x1181_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2711_123x1181_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2711_123x1181_2006.phy_RAXML