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 601 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 602 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 603 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 604 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 605 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 606 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 607 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 608 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 612 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 613 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 614 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 615 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 616 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 617 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 618 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 619 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 620 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 621 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 622 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 623 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Sequences tax4 and tax10 are exactly identical IMPORTANT WARNING: Sequences tax4 and tax14 are exactly identical IMPORTANT WARNING: Sequences tax5 and tax7 are exactly identical IMPORTANT WARNING: Sequences tax5 and tax13 are exactly identical IMPORTANT WARNING: Sequences tax9 and tax11 are exactly identical IMPORTANT WARNING: Sequences tax23 and tax24 are exactly identical IMPORTANT WARNING: Sequences tax37 and tax39 are exactly identical IMPORTANT WARNING: Sequences tax41 and tax44 are exactly identical IMPORTANT WARNING: Sequences tax52 and tax55 are exactly identical IMPORTANT WARNING: Sequences tax66 and tax77 are exactly identical IMPORTANT WARNING: Sequences tax70 and tax71 are exactly identical IMPORTANT WARNING: Sequences tax70 and tax73 are exactly identical IMPORTANT WARNING Found 12 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. IMPORTANT WARNING Found 28 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_M2716_79x1252_2006.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 280 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.478677 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): 0.223004 pi(C): 0.303552 pi(G): 0.244211 pi(T): 0.229232 1.528992 -3361.402469 2.424502 -3360.463678 4.453060 -3360.462656 7.763214 -3360.462656 12.174808 -3356.225195 15.244814 -3354.899486 19.385461 -3353.745050 22.245163 -3353.542747 24.624092 -3353.458221 27.767581 -3353.378014 31.847582 -3353.378014 36.337504 -3346.866955 Overall Time for 1 Inference 36.351972 Likelihood : -3346.866955 Parsimony starting tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_parsimonyTree.nucleic_M2716_79x1252_2006.phy_RAXML Final tree written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_result.nucleic_M2716_79x1252_2006.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_log.nucleic_M2716_79x1252_2006.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_nucl_raxml/./RAxML_info.nucleic_M2716_79x1252_2006.phy_RAXML