IMPORTANT WARNING: Alignment column 395 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 396 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 397 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 398 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 399 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 400 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 401 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 402 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 403 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 404 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 405 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 406 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 407 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 408 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 409 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 410 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 411 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 412 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 413 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 414 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 415 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 416 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 417 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 418 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 420 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 421 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 422 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 423 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 424 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 425 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 426 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 427 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 428 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 Found 35 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 undetermined columns removed is printed to file /auto/dufayard/res/ori_prot_raxml/proteic_M2304_31x429_2005.phy.reduced You are using RAxML version 7.0.4 released by Alexandros Stamatakis in April 2008 Alignment has 305 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.117528 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: AA Substitution Matrix: WAG Fixed Base Frequencies: pi(A): 0.087000 pi(R): 0.044000 pi(N): 0.039000 pi(D): 0.057000 pi(C): 0.019000 pi(Q): 0.037000 pi(E): 0.058000 pi(G): 0.083000 pi(H): 0.024000 pi(I): 0.049000 pi(L): 0.086000 pi(K): 0.062000 pi(M): 0.020000 pi(F): 0.038000 pi(P): 0.046000 pi(S): 0.070000 pi(T): 0.061000 pi(W): 0.014000 pi(Y): 0.035000 pi(V): 0.071000 3.896573 -5510.735353 22.819472 -5507.955124 56.550015 -5507.955124 110.167655 -5505.549330 182.461974 -5505.549330 247.150262 -5505.549330 303.615195 -5505.549330 341.525731 -5505.549330 342.324999 -5505.549330 347.304190 -5505.539649 Overall Time for 1 Inference 347.319751 Likelihood : -5505.539649 Parsimony starting tree written to: /auto/dufayard/res/ori_prot_raxml/./RAxML_parsimonyTree.proteic_M2304_31x429_2005.phy_RAXML Final tree written to: /auto/dufayard/res/ori_prot_raxml/./RAxML_result.proteic_M2304_31x429_2005.phy_RAXML Execution Log File written to: /auto/dufayard/res/ori_prot_raxml/./RAxML_log.proteic_M2304_31x429_2005.phy_RAXML Execution information file written to: /auto/dufayard/res/ori_prot_raxml/./RAxML_info.proteic_M2304_31x429_2005.phy_RAXML 343.56user 0.00system 5:47.33elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps