Set Pipeline Parameters

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Description

Sets size limits, threshold values and other parameters that control the flow along the pipeline.

Usage

1

Arguments

...

arguments in tag = value form. The tags must come from the names of graphical parameters described in the 'Parameters' section.

Value

a list of parameters described in the 'Parameters' section.

Parameters

update.seqs

currently unused.

max.gi.per.spec

numeric, giving the maximum number of sequences that will be used per species. Can be used to avoid model organism (e.g., rice, Drosophila, ...) cluttering up the pipeline with thousands of sequences (default: 100).

max.bp

numeric, the maximal length of DNA sequences in base pairs to be included in the alignment. The upper limit is determined by the alignment program and the specific alignment and can only be determined by trial-and-error (default: 5000).

reference.stringence

currently unused.

reference.max.dist

currently unused.

min.seqs.reference

currently unused.

max.dist

numeric, ranging between 0 and 1. The sequences from taxa for which only a single accession is available will be included only if their genetic distance (measured as the fraction of divergent nucleotide poistions) is less then max.dist (default: 0.5)

fract.miss

numeric, ranging between 0 and 1. To avoid long stretches of only a few sequences at the beginning and the ending of an alignment block a minimum required number of sequences can be set as a fraction of the total number of sequences in this alignment block. Has been superseeded by the gb.* parameters.

filter1

currently unused.

filter2

currently unused.

filter3

currently unused.

filter4

currently unused.

block.max.dist

numeric, ranging between 0 and 1. block.max.dist gives the maximum genetic distance (measured as the fraction of divergent nucleotide positions) allowed in a sequence alignment block. The alignment of individual marker is iteratively broken into smaller blocks until this condition is met with.

min.n.seq

numeric, the minimum number of sequences required for an alignment block. Alignment blocks with less than min.n.seq are dropped from the output.

gb1, gb2, gb3, gb4, gb5

parameters for masking of alignment blocks with gblocks.

Author(s)

Christoph Heibl

See Also

megapteraProj for creating a megaptera project.

Examples

1