pmp_bf [options] <tree> <motif>
This utility calculates the statistical power of a phylogenetic motif model.
A file containing a phylogenetic tree in Newick format.
A file containing MEME formatted motifs. Outputs from MEME and DREME are supported along with minimal MEME format for which there are conversion scripts available to support other formats.
Prints the false positive and false negative rate at each of 10000 score values to standard output.
Each line of the output has the following:
|--hb||Use the Halpern-Bruno modification to the evolutionary model.|
|--model||single|average|jc|k2|f81|f84|hky|tn||The evolutionary model to use.
|Behaves as if --model f81 was specified.|
|--pur-pyr||ratio||The ratio of the purine transition rate to pyrimidine transition rate. This parameter is used by the Tamura-nei model.||The ratio is set to 1.0.|
|--transition-transversion||ratio||The ratio of the transition rate to the transversion rate. This parameter is used by the Kimura 2-parameter, F84, HKY, and Tamura-nei models.||The ratio is set to 0.5.|
|--bg||rate||The mutation rate for sites in the background model.||The background mutation rate is set to 1.|
|--fg||rate||The mutation rate for sites in the foreground model(s).||The mutation rate is set to 1.|
|--motif||ID||Use only the motif identified by ID. This option may be repeated.|
|--bgfile||The file should be in MEME background file format.
||Use frequencies embedded in the application from the non-redundant database.|
|--pseudocounts||A pseudocount to be added to each count in the motif matrix, weighted by the background frequencies for the nucleotides (Dirichlet prior), before converting the motif to probabilities.||The pseudocount is set to 0.1.|
|--ustar||target||Convert the tree into a uniform star tree with the target sequence at its center.|