Gibbs program: parameters' description.
GibbsDNA Sites and Motif Sampler is the simple modification of original
Gibbs Sampler (see Neuwald AF, et al.
and Lawrence CE , et al. )
adjusted for DNA sequence analysis. Several options have been added and the work is still in progress.
Sites sampler
file lengths [options]
Motif sampler
file lengths expect [options]
lengths = [,]: lengths of elements for each type
expect = [,]: expected number of elements for each type
[,] = numbers for each element (e.g. "10,12,15" for 3 types)
Options:
-C prob. cutoff (0 < C <= 1) for near optimum sampling [real]
-c number of cycles between shifts (sites sampler)
or maximum number of cycles per run (motif sampler) [int]
-d DON'T use fragmentation (i.e., column sampler)
-f create a scan output file (file.sn)
-I interactively specify #sites/sequence (sites sampler)
(default: one site of each type per sequence)
-L set rapid convergence limit (higher = longer to converge) [int]
-m set maximum number of cycles in each run (sites sampler) [int]
-o use element order in probabilities (sites sampler)
(each sequence must contain the same number of elements)
-p number of pseudo counts for product multinomial model [float]
-q pseudo counts for ordering model (sites sampler) [float]
-R set number of near-optimum readings taken [int]
-r randomly shuffle input sequences
-s give seed for random number generator [int]
-t maximum number of sampling runs [int]
-w output wilcoxon rank test information (motif sampler)
-W set fractional weight (0 to 1.0) on priors (motif sampler) [float]
-b1 include both strands as single sequence
-b2 include both strands as separate sequences
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