1.2.2 construction of phylogenetic trees of DNA sequences using maximum likelihood Olsen, Matsuda, Hagstrom, Overbeek Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10: 41-48. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376. phylogeny fastdnaml fastdnaml perl ($bootstrap)? "cat > $alignment.tmp;" : "fastDNAml" 1000 clean_tmp perl "; clean_checkpoints" 1100 alignment Sequence Alignment File perl "cat $value | " 1 The input to fastDNAml is similar to that used by DNAML (and the other PHYLIP programs). 12 readseq_ok_alig perl fastDNAml inputopt Input Options frequencies Instructs the program to use empirical base frequencies derived from the sequence data perl (! $value)? "frequencies $fA $fC $fG $fT | " : "" 1 2 fA frequency of A (instead of empirical frequencies) perl "" 0.25 1 perl ! $frequencies fC frequency of C (instead of empirical frequencies) perl "" 0.25 1 perl ! $frequencies fG frequency of G (instead of empirical frequencies) perl "" 0.25 1 perl ! $frequencies fT frequency of T (instead of empirical frequencies) perl "" 0.25 1 perl ! $frequencies outgroup Use the specified sequence number for the outgroup perl ($value)? "outgroup $value | " : "" 2 transition ratio of transition to transversion type substitutions perl ($value && $value!=$vdef)? "transition $value | " : "" 2.0 2 This option with a value of 2.0 (the program's default value) can be used before a global or treefile option with auxiliary data. perl ! ($global && ($final_arrgt||$partial_arrgt)) jumble Randomize the sequence addition order (jumble) perl ($value)? "jumble | " : "" 2 Note that fastDNAml explores a very small number of alternative tree topologies relative to a typical parsimony program. There is a very real chance that the search procedure will not find the tree topology with the highest likelihood. Altering the order of taxon addition and comparing the trees found is a fairly efficient method for testing convergence. Typically, it would be nice to find the same best tree at least twice (if not three times), as opposed to simply performing some fixed number of jumbles and hoping that at least one of them will be the optimum. perl ! $bootstrap non_interleaved Interleaved format perl ($value)? "" : "non_interleaved | " 1 2 bootopt Bootstrap Options bootstrap generates a re-sample of the input data (bootstrap) perl ($value)? "fastDNAml_boot_web -out " : "" 1001 tree files will be summarized in one '.tree' file as well as output files in one '.out' file nboots how many samples perl ($value && $value != $vdef)? " -boots $value" : "" 1 1002 more than 1000 samples is not possible on this server perl $value > 1000 perl $bootstrap bootstrap_seed random number seed for bootstrap perl ($value)? " -seed $value" : "" 1002 Warning: For a given random number seed, the sample will always be the same. perl $bootstrap nbest nbest: input order is jumbled (up to maxjumble times) until same tree is found n_best times perl " $value" 2 1004 perl $bootstrap maxjumble maximum attempts at replicating inferred tree (max jumble) perl ($value)? " -max $value" : "" 10 1002 perl $bootstrap concat perl " && (concattree $alignment.tree.tmp $alignment.out.tmp ; mv $alignment.tree.tmp $alignment.tree; mv $alignment.out.tmp $alignment.out) " 1010 perl $bootstrap in_file perl " $alignment.tmp" 1003 perl $bootstrap bootfiles perl $bootstrap *.tree *.out *.tmp outputopt Output and Results Options outfile Output File perl ($value && $value ne $vdef) ? " > $outfile" : "" fastdnaml.out perl ! $bootstrap 1010 treefile Save tree in treefile perl (!$value)? "treefile | " : "" 1 2 perl ! $bootstrap printdata Echo of the data in addition to the usual output (printdata) perl ($value)? "printdata | " : "" 1 2 tmpfiles treefile.* tmpaligfiles "$alignment.tmp_*" arrgtopt Rearrangements Options quickadd Decreases the time in initially placing a new sequence in the growing tree (quickadd) perl (! $value)? "quickadd | " : "" 1 2 This option greatly decreases the time in initially placing a new sequence in the growing tree (but does not change the time required to subsequently test rearrangements). The overall time savings seems to be about 30%, based on a very limited number of test cases. Its downside, if any, is unknown. This will probably become default program behavior in the near future. If the analysis is run with a global option of 'G 0 0', so that no rearrangements are permitted, the tree is build very approximately, but very quickly. This may be of greatest interest if the question is, 'Where does this one new sequence fit into this known tree?' The known tree is provided with the restart option, below. PHYLIP DNAML does not include anything comparable to the quickadd option. global global rearrangements perl ($value && (((defined $final_arrgt || defined $partial_arrgt) && ($trans_cmd = "transition $transition |")) || 1))? "$trans_cmd global $final_arrgt $partial_arrgt | " : "" 3 The G (global) option has been generalized to permit crossing any number of branches during tree rearrangements. In addition, it is possible to modify the extent of rearrangement explored during the sequential addition phase of tree building. The G U (global and user tree) option combination instructs the program to find the best of the user trees, and then look for rearrangements that are better still. If a rearrangement distance is specified, the input must contain a transition option. The Global option can be used to force branch swapping on user trees, (combination of Global and User Tree(s) options). If a rearrangement distance is specified, the input must contain a bootstrap, a jumble or a transition option. perl ((defined $final_arrgt||defined $partial_arrgt) && !($transition||$bootstrap||$jumble)) final_arrgt number of branches to cross in rearrangements of the completed tree perl "" 2 partial_arrgt number of branches to cross in testing rearrangements during the sequential addition phase of tree inference perl "" 2 categopt Categories and Weights Options categories categories file perl ($value)? "categories $value |" : "" 2 The data must have the format specified for PHYLIP dnaml 3.3. The first line must be the letter C, followed by the number of categories (a number in the range 1 through 35), and then a blank-separated list of the rates for each category. (The list can take more than one line; the program reads until it finds the specified number of rate values.) The next line should be the word Categories followed by one rate category character per sequence position. The categories 1 - 35 are represented by the series 1, 2, 3, ..., 8, 9, A, B, C, ..., Y, Z. These latter data can be on one or more lines. For example: C 12 0.0625 0.125 0.25 0.5 1 2 4 8 16 32 64 128 Categories 5111136343678975AAA8949995566778888889AAAAAA9239898629AAAAA9 Category 'numbers' are ordered: 1, 2, 3, ..., 9, A, B, ..., Y, Z. Category zero (undefined rate) is permitted at sites with a zero in a user-supplied weighting mask. weights weights file (user-specified column weighting information) perl ($value)? "weights $value |" : "" 2 example: Weights 111111111111001100000100011111100000000000000110000110000000 In case of bootstrap, only positions that have nonzero weights are used in computing the bootstrap sample. weights_categories Adds both the userweights and categories from a file perl ($value)? "weights_categories $value |" : "" 2 treeopt User input Tree Options perl ! $bootstrap This options allows you to enter your own trees and instructs the program to evaluate them. user_tree User tree - tree(s) file perl ($value && (! $user_lengths|| ($L="L") ))? "usertree $value $L|" : "" 2 The trees must be in Newick format, and terminated with a semicolon. (The program also accepts a pseudo_newick format, which is a valid prolog fact.) The tree reader in this program is more powerful than that in PHYLIP 3.3. In particular, material enclosed in square brackets, [ like this ], is ignored as comments; taxa names can be wrapped in single quotation marks to support the inclusion of characters that would otherwise end the name (i.e., '(', ')', ':', ';', '[', ']', ',' and ' '); names of internal nodes are properly ignored; and exponential notation (such as 1.0E-6) for branch lengths is supported. perl ! $bootstrap user_lengths user trees to be read with branch lengths perl "" Causes user trees to be read with branch lengths (and it is an error to omit any of them). Without the L option, branch lengths in user trees are not required, and are ignored if present. perl ! $bootstrap tree *tree* phylip_tree perl 1