Class for pipeline parameters of
Objects can be created by calls of the form
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).
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).
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)
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
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.
numeric, the minimum number of sequences required for an alignment block. Alignment blocks with less than
min.n.seq are dropped from the output.
parameters for masking of alignment blocks with
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