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megaptera (version 1.0-0)

stepH: Step H: Detect and Separate Unalignable Blocks

Description

Dependent on the substitution rate of the genomic region and the taxonomic depth of the study group, not always all accession can be aligned into a single alignment. step H will detect and separate such unalignable alignment blocks.

Usage

stepH(x, clean = TRUE)

Arguments

x
an object of class megapteraProj.
clean
logical: do cleaning/masking of alignment blocks?

Value

  • None. stepA is called for its side effects

See Also

megapteraProj; stepF for the preceeding step and supermatrix for the concatenation of loci.