stepH: Step H: Detect and Separate Unalignable Blocks
In heibl/megaptera: MEGAPhylogeny Techniques in R
Description
Usage
Arguments
Value
References
See Also
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
1
stepH(x, max.mad)
Arguments
x
An object of class megapteraProj.
max.mad
Numeric, giving the treshold value for the assessment of
saturation: alignments with a median average distance (MAD) of
max.mad or greater will be broken into blocks. The default value of
0.01 has been estimated with simulation by Smith et al. (2009).
Value
None, stepH is called for its side effects.
References
Smith, S. A., J. M. Beaulieu, and M. J. Donoghue. 2009.
Mega-phylogeny approach for comparative biology: an alternative to
supertree and supermatrix approaches. BMC Evolutionary Biology
9:37.
See Also
megapteraProj; stepMAFFT for the preceeding
step and supermatrix for the concatenation of loci.
heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.
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Description Usage Arguments Value References See Also
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
1 | stepH(x, max.mad)
|
Arguments
x |
An object of class |
max.mad |
Numeric, giving the treshold value for the assessment of
saturation: alignments with a median average distance (MAD) of
|
Value
None, stepH is called for its side effects.
References
Smith, S. A., J. M. Beaulieu, and M. J. Donoghue. 2009. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evolutionary Biology 9:37.
See Also
megapteraProj; stepMAFFT for the preceeding
step and supermatrix for the concatenation of loci.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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