BAMBE 2.03b Bayesian Analysis in Molecular Biology and Evolution Simon, Larget Larget, B. and D. Simon (1999). Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution 16:750-759. Simon, D. and B. Larget. 1998. Bayesian analysis in molecular biology and evolution (BAMBE), version 1.01 beta. Department of Mathematics and Computer Science, Duquesne University. phylogeny bambe bambe perl "bambe < bamberc" 0 rcfile bamberc data_file Alignment file (data-file) perl "data-file=$value\\n" bamberc 6 readseq_ok_alig perl 1 bambe_format Alignement file in BAMBE format ? perl ($value) ? "" : "cp $data_file $data_file.orig; fmtseq -f21 -p < $data_file.orig > $data_file; " 0 -10 run_options Run characteristics 1 seed Seed for random number generator (seed) perl (defined $value && $value != $vdef)? "seed=$value\\n" : "" 194024933 bamberc cycles Number of cycles to run the main algorithm (cycles) perl (defined $value && $value != $vdef)? "cycles=$value\\n" : "" 6000 bamberc main_algorithm Algorithm to run during production cycles (main-algorithm) perl ($value && $value ne $vdef)? "main-algorithm=$value\\n" : "" local global local bamberc burn Number of cycles to run the burn algorithm (burn) perl (defined $value && $value != $vdef)? "burn=$value\\n" : "" 1000 Parameter values are not updated during burn. User should discard these cycles and the initial cycles of the main algorithm before inference. bamberc burn_algorithm Algorithm to run during burn (burn-algorithm) perl ($value && $value ne $vdef)? "burn-algorithm=$value\\n" : "" global global local bamberc use_beta Use scaled beta distribution modification of the local algorithm (use-beta) perl ($value) ? "use-beta=true\\n" : "" 0 bamberc perl $main_algorithm eq "local" || $burn_algorithm eq "local" model_options Model specification 2 molecular_clock Use a molecular clock (molecular-clock) perl ($value)? "" : "molecular-clock=false\\n" 1 bamberc likelihood_model Likelihood model (molecular-clock) perl ($value && $value ne $vdef) ? "likelihood-model=$value\\n" : "" HKY85 HKY85 F84 TN93 bamberc category_list A valid category list (category-list) perl ($value)? "category-list=$value\\n" : "" Each category has its own set of parameters. Each category is denoted by a positive integer between 1 and 10. A comma-separated list gives the categories of the sites in order, e.g., 1,2,3,1,3 means that the first site is in category 1, the second in 2, the third in 3, the fourth in 1, and the fifth site is in category 3. A repeat count is indicated by a caret (^). For example, 1^20,2^5,3^2 means that the first twenty sites are in category 1, the next five sites are in 2, and the next two sites are in category 3. Parentheses may be used to group sites together with a common repeat count, i.e., (1,2)^5 is the same as 1,2,1,2,1,2,1,2,1,2. Repeat counts may be nested, e.g., (1^3,2)^2 is the same as 1,1,1,2,1,1,1,2. Repetition to the end of the list of sites is indicated by an asterisk (*). For example, 1^5,2* means that the first five sites are in category 1, and all the remaining sites are in category 2. Parentheses may also be used in conjunction with the asterisk, e.g., (1,2)* is the same as 1,2,1,2,1,2,.... The category list may contain at most one asterisk and it must be associated with the last category or group in the list. In other words, an asterisk may appear only at the end of the list. Examples 1* - all sites are the same category. (default) (1,2,3)* - all sites are partitioned by codon position. 1^99,2^50,3^9 - the sites are divided over three genes. Each gene has its own set of parameters used by all sites in that gene. The first gene is composed of the first ninety-nine sites, the next by the next fifty sites, and the last by nine sites. bamberc 20 single_kappa Single kappa (single-kappa) perl ($value)? "single-kappa=true\\n" : "" 0 If true, the same kappa parameter is used for all site categories. If false, there are different values for different site categories. It has no effect if there is only one rate category. bamberc initial_kappa Comma separated list of positive kappa values (initial-kappa) perl ($value && $value ne $vdef)? "initial-kappa=$value\\n" : "" 2.0,2.0,2.0 If single-kappa is true, a warning is given if more than one value is specified. The first value will be used. If single-kappa is false, a value must be specified for each category in use. bamberc 20 initial_theta Comma separated list of positive theta values (initial-theta) perl ($value && $value ne $vdef)? "initial-theta=$value\\n" : "" 1.0,1.0,1.0 The weighted average of these values should be 1, with weights given by the proportion of sites in each site category. (Renormalization is automatic and a warning given if the condition fails.) If there are an equal number of sites in each category, for example, the numbers should average to 1. bamberc 20 estimate_pi Use empirical relative frequencies (estimate-pi) perl ($value) ? "" : "estimate-pi=false\\n" 1 If ture, the initial stationary probabilities for each base in each category are estimated by the relative frequencies with which they appear in the data. bamberc initial_pia Comma separated list of initial stationary probability of base A (initial-pia) perl (defined $value && $value != $vdef) ? "initial-pia=$value\\n" : "" 0.25,0.25,0.25 perl ! $estimate_pi 20 initial_pig >Comma separated list of initial stationary probability of base G (initial-pig) perl (defined $value && $value != $vdef) ? "initial-pig=$value\\n" : "" 0.25,0.25,0.25 perl ! $estimate_pi 20 initial_pic >Comma separated list of initial stationary probability of base C (initial-pia) perl (defined $value && $value != $vdef) ? "initial-pic=$value\\n" : "" 0.25,0.25,0.25 perl ! $estimate_pi 20 initial_pit >Comma separated list of initial stationary probability of base T (initial-pia) perl (defined $value && $value != $vdef) ? "initial-pit=$value\\n" : "" 0.25,0.25,0.25 perl ! $estimate_pi 20 initial_ttp Comma separated list of positive transition/transversion parameter values (TN93 model) (initial-ttp) perl ($value && $value ne $vdef)? "initial-ttp=$value\\n" : "" 1.0,1.0,1.0 20 perl $likelihood_model eq "TN93" bamberc This is used only with TN93. There must be a value specified for each site-category used if TN93 is the chosen model. initial_gamma Comma separated list of positive gamma values ((TN93 model) (initial-gamma) perl ($value && $value ne $vdef)? "initial-gamma=$value\\n" : "" 1.0,1.0,1.0 perl $likelihood_model eq "TN93" bamberc 20 This is used only with TN93. There must be a value specified for each site-category used if TN93 is the chosen model. param_update Parameter updating 4 parameter_update_interval Parameter update interval (parameter-update-interval) perl (defined $value && $value != $vdef)? "parameter-update-interval=$value\\n" : "" 1 During the main algorithm, any 'on' parameters are updated at each cycle divisible by this value. Use zero for no paramter updating. bamberc update_kappa Update kappa value (update-kappa) perl ($value)? "" : "update-kappa=false\\n" 1 bamberc update_theta Update theta value (update-theta) perl ($value)? "" : "update-theta=false\\n" 1 bamberc update_pi Update pi value (update-pi) perl ($value)? "" : "update-pi=false\\n" 1 bamberc update_ttp Update tpp value (TN93 model) (update-ttp) perl ($value)? "" : "update-ttp=false\\n" 1 bamberc perl $likelihood_model eq "TN93" update_gamma Update gamma value for (TN93 model) (update-gamma) perl ($value)? "" : "update-gamma=false\\n" 1 bamberc perl $likelihood_model eq "TN93" tuning_options Tuning parameters 5 tune_interval Tune interval (tune-interval) perl (defined $value && $value != $vdef)? "tune-interval=$value\\n" : "" 200 While running global during the burn, if the acceptance rate for tree proposal falls below 15% during this interval, delta is halved. bamberc global_tune Half-window width for global (global-tune) perl (defined $value && $value != $vdef)? "global-tune=$value\\n" : "" 0.01 This tuning parameter is only used with the global algorithm during burn. The smaller its value, the greater the tree acceptance rate will be. bamberc perl $burn_algorithm =~ /^global/ local_tune Stretch parameter for local (local-tune) perl (defined $value && $value != $vdef) ? "local-tune=$value\\n" : "" 0.19 perl $burn_algorithm =~ /^global/ || $main_algorithm =~ /^global/ bamberc This tuning parameter is only used with the local algorithm. It modulates the size of a maximal stretch. The smaller the value, the greater the tree acceptance rate will be. theta_tune Dirichlet parameter for theta update (theta-tune) perl (defined $value && $value != $vdef)? "theta-tune=$value\\n" : "" 2000.0 Tuning parameter used during update of theta value(s). The larger its value, the more likely proposals are to be accepted. bamberc pi_tune Dirichlet parameter for pi update (pi-tune) perl (defined $value && $value != $vdef)? "pi-tune=$value\\n" : "" 2000.0 Tuning parameter used during update of pi values. The larger its value, the more likely proposals are to be accepted. bamberc kappa_tune Halft window width for kappa update (kappa-tune) perl (defined $value && $value != $vdef)? "kappa-tune=$value\\n" : "" 0.1 perl $parameter_update_interval > 0 && $update_kappa bamberc This tuning parameter is only used when 'parameter-update-interval' is positive and 'update-kappa' is true. The smaller its value, the greater the parameter acceptance rate will be. ttp_tune Halft window width for tpp update (TN93 model) (tpp-tune) perl (defined $value && $value != $vdef)? "tpp-tune=$value\\n" : "" 0.1 perl $parameter_update_interval > 0 && $update_tpp bamberc This tuning parameter is only used when 'parameter-update-interval' is positive and 'update-tpp' is true. The smaller its value, the greater the parameter acceptance rate will be. gamma_tune Half window width for gamma update (TN93 model) (gamma-tune) perl (defined $value && $value != $vdef) ? "gamma-tune=$value\\n" : "" 0.1 perl $parameter_update_interval > 0 && $update_gamma bamberc This tuning parameter is only used when 'parameter-update-interval' is positive and 'update-gamma' is true. The smaller its value, the greater the parameter acceptance rate will be. beta_tune Beta parameter for local update (beta-tune) perl (defined $value && $value != $vdef)? "beta-tune=$value\\n" : "" 10.0 perl $use_beta bamberc This tuning parameter is only used if the 'use-beta' is true. The larger its value, the greater the parameter acceptance rate will be. output_options Output options 2 sample_interval Sample interval (sample-interval) perl (defined $value && $value != $vdef)? "sample-interval=$value\\n" : "" 200 During burn and main algorithms, the tree topology, log likelihoods, and parameters are written to files at each cycle divisible by this value. bamberc newick_format Newick format of tree file (newick-format) perl ($value)? "" : "newick-format=false\\n" 1 Indicates the format of the tree to read (if not random) and the format of the tree to print after the run. bamberc results_files results.lpd results.par results.out result_tree results.tre phylip_tree perl $newick_format top_file results.top file_root perl "file-root=results\\n" 6 bamberc input_options Input options 7 outgroup Outgroup perl (defined $value && $value != $vdef)? "outgroup=$value\\n" : "" 1 perl ! $molecular-clock bamberc This is ignored if a molecular clock is assumed. In the absence of a clock, trees and tree topologies are printed with the outgroup emerging directly from the root. tree_file Tree file (tree-file) perl ($value)? "tree-file=$value\\n" : "" If no tree file is given, the program generates a random tree from a flat distribution where each labeled history is equally likely. bamberc init_tree_type Initial tree type (initial-tree-type) random random upgma neighbor-joining newick bambe bamberc . random select a tree from the prior . upgma sets the initial clock tree to the UPGMA tree using maximum likelihodd distances with the specified model and initial parameter values. . neighbor-joining sets the initial nonclock tree to the neigbor joining tree using maximum liklihodd distances with the specified model and initial parameter values. . newick reads in an initial tree in Newick format from a file. . bambe reads in an initial tree in BAMBE format from a file. max_initial_tree_height Initial tree height used to generate an initial random tree (max-initial-tree-height) perl (defined $value && $value != $vdef)? "max-initial-tree-height=$value\\n" : "" 0.1 bamberc This parmeter is only used to generate an initial random tree.