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 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 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 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 154 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 250 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 429 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 477 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 478 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 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 786 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 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 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 tax4 and tax5 are exactly identical IMPORTANT WARNING: Sequences tax4 and tax8 are exactly identical IMPORTANT WARNING: Sequences tax22 and tax24 are exactly identical IMPORTANT WARNING: Sequences tax27 and tax29 are exactly identical IMPORTANT WARNING: Sequences tax34 and tax42 are exactly identical IMPORTANT WARNING: Sequences tax34 and tax43 are exactly identical IMPORTANT WARNING: Sequences tax38 and tax40 are exactly identical IMPORTANT WARNING: Sequences tax47 and tax48 are exactly identical IMPORTANT WARNING: Sequences tax51 and tax56 are exactly identical IMPORTANT WARNING: Sequences tax76 and tax81 are exactly identical IMPORTANT WARNING: Sequences tax76 and tax83 are exactly identical IMPORTANT WARNING: Sequences tax76 and tax100 are exactly identical IMPORTANT WARNING: Sequences tax76 and tax101 are exactly identical IMPORTANT WARNING: Sequences tax77 and tax79 are exactly identical IMPORTANT WARNING: Sequences tax116 and tax120 are exactly identical IMPORTANT WARNING: Sequences tax116 and tax122 are exactly identical IMPORTANT WARNING: Sequences tax116 and tax124 are exactly identical IMPORTANT WARNING: Sequences tax117 and tax127 are exactly identical IMPORTANT WARNING Found 18 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. IMPORTANT WARNING Found 73 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_M2916_143x897_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 303 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.107943 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): 0.167880 pi(C): 0.312461 pi(G): 0.273166 pi(T): 0.246493 1.491526 -3533.553758 3.286726 -3515.743575 7.535262 -3506.410599 14.833696 -3503.626291 26.193457 -3491.928043 30.512497 -3490.045078 39.066361 -3488.606843 46.718486 -3488.456003 52.275517 -3488.362461 58.035946 -3488.272614 68.310137 -3488.186202 80.177894 -3488.186202 91.613269 -3464.554661 Overall Time for 1 Inference 91.638408 Likelihood : -3464.554661 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2916_143x897_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2916_143x897_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2916_143x897_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2916_143x897_2006.phy_RAXML