IMPORTANT WARNING: Alignment column 38 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 46 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 233 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 234 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 235 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 236 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 237 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 238 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 239 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 241 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 242 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 243 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 244 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 245 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 246 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 247 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 248 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 249 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 524 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 525 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 526 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 527 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 528 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 529 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 530 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 531 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 532 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 533 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 534 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 535 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 536 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 537 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 538 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 539 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 540 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 541 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 542 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 567 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 568 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 569 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 570 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 571 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 572 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 573 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 574 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 575 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 576 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 577 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 578 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 579 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 745 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Sequences tax7 and tax454 are exactly identical IMPORTANT WARNING: Sequences tax15 and tax16 are exactly identical IMPORTANT WARNING: Sequences tax247 and tax248 are exactly identical IMPORTANT WARNING: Sequences tax287 and tax288 are exactly identical IMPORTANT WARNING: Sequences tax443 and tax444 are exactly identical IMPORTANT WARNING Found 5 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. IMPORTANT WARNING Found 52 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/bigdatasets_raxml_nucl/nucleic_M2839_470x829_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 733 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.248076 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): 0.277334 pi(C): 0.194368 pi(G): 0.283188 pi(T): 0.245110 35.075609 -42639.382101 51.317149 -42510.258549 103.134669 -42476.962976 219.143442 -42452.200459 422.245469 -42452.199857 724.607834 -42316.228380 798.402209 -42257.476122 865.178511 -42241.926470 928.634310 -42231.949288 975.320623 -42230.222652 1000.163946 -42230.128936 1092.993579 -42218.697225 1155.536621 -42218.610246 1251.411422 -42214.407517 1349.313453 -42214.325346 1434.448950 -42214.250722 1590.098567 -42214.179048 1858.710346 -42214.179048 1928.238902 -42205.833422 Overall Time for 1 Inference 1928.291250 Likelihood : -42205.833422 Parsimony starting tree written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_parsimonyTree.nucleic_M2839_470x829_2006.phy_RAXML Final tree written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_result.nucleic_M2839_470x829_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_log.nucleic_M2839_470x829_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/bigdatasets_raxml_nucl/./RAxML_info.nucleic_M2839_470x829_2006.phy_RAXML