IMPORTANT WARNING: Alignment column 42 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 49 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 55 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 67 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 68 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 69 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 70 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 77 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 78 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 79 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 80 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 81 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 82 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 97 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 98 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 105 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 112 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 134 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 136 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 146 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 147 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 148 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 165 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 166 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 179 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 224 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 240 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 299 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 419 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 429 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 484 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 485 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 486 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 487 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 488 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 489 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 490 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 491 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 492 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 493 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 494 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 495 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 496 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 497 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 498 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 499 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 500 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 501 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 502 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 503 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 511 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 512 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 513 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 514 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 515 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 516 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 609 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 668 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 669 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 670 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 676 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 691 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 692 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 693 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 694 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 707 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 708 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 709 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 710 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 711 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 722 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 773 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 776 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 777 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 786 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 846 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 847 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 851 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 854 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: Alignment column 888 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 889 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Sequences tax8 and tax11 are exactly identical IMPORTANT WARNING: Sequences tax16 and tax20 are exactly identical IMPORTANT WARNING: Sequences tax52 and tax54 are exactly identical IMPORTANT WARNING: Sequences tax72 and tax75 are exactly identical IMPORTANT WARNING Found 4 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. IMPORTANT WARNING Found 84 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_M2913_81x897_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 197 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.105551 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): 0.164486 pi(C): 0.294572 pi(G): 0.268290 pi(T): 0.272652 0.473663 -2446.025750 1.152939 -2433.569376 2.651666 -2432.494615 4.926855 -2432.313631 8.069965 -2428.195804 10.916447 -2425.567093 12.854096 -2425.346526 15.984477 -2424.384733 18.155351 -2424.289946 20.152426 -2424.200703 23.032162 -2424.024489 26.489994 -2423.944503 29.025233 -2423.868602 31.906526 -2423.739390 34.688694 -2423.739390 37.526907 -2412.243042 Overall Time for 1 Inference 37.543376 Likelihood : -2412.243042 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2913_81x897_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2913_81x897_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2913_81x897_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2913_81x897_2006.phy_RAXML