pmp_bf

Usage:

pmp_bf [options] <tree> <motif>

Description

This utility calculates the statistical power of a phylogenetic motif model.

Input

Tree File

A file containing a phylogenetic tree in Newick format.

Motif File

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.

Output

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:

Motif ID score score FPR False Positive Rate TPR True Positive Rate

Options

Option Parameter Description Default Behaviour
General Options
--hb Use the Halpern-Bruno modification to the evolutionary model.
--modelsingle|​average|​jc|​k2|​f81|​f84|​hky|​tn The evolutionary model to use.
ValueNameDescription
singleSingle Score score first sequence: compute standard log-odds score of first sequence in the alignment; ignores tree but does NOT remove gaps.
averageAverage Score compute average of standard log-odds score of aligned sites.
jcJukes-Cantor equilibrium base frequencies are all 1/4; the only free parameter is the mutation rate.
k2Kimura 2-parameter equilibrium base frequencies are all 1/4; the free parameters are the mutation rate and the transition/transversion rate ratio.
f81Felsenstein 1981 equilibrium base frequencies are taken from the alignment; the only free parameter is the mutation rate.
f84Felsenstein 1984 equilibrium base frequencies are taken from the alignment; the free parameters are the mutation rate and the transition/transversion rate ratio. The ratio of purine-purine to pyrimidine->pyrimidine transitions is assumed to be 1.
hkyHasegawa-Kishino-Yano equilibrium base frequencies are taken from the alignment; the free parameters are the mutation rate and the transition/transversion rate ratio. The ratio of purine-purine to pyrimidine-pyrimidine transitions is assumed to be equal to the ratio of purines to pyrimidines.
tnTamura-Nei equilibrium base frequencies are taken from the alignment; the free parameters are the mutation rate, the transition/transversion rate ratio, and the ratio of purine-purine transitions to pyrimidine-pyrimidine transitions.
A description of the f81 model is available in chapter 13 of Statistical Methods in Bioinformatics by Ewens and Grant. The other models are described in chapters 9 and 13 of Inferring Phylogenies by Felsenstein. 		Behaves as if --model f81 was specified.
--pur-pyrratio 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-transversionratio 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.
--bgrate The mutation rate for sites in the background model. The background mutation rate is set to 1.
--fgrate The mutation rate for sites in the foreground model(s). The mutation rate is set to 1.
--motifID Use only the motif identified by ID. This option may be repeated.
--bgfile The file should be in MEME background file format. The keyword motif-file can be used to indicate that the frequencies should be taken from the motif file. 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.
--ustartarget Convert the tree into a uniform star tree with the target sequence at its center.