msa_set_scoreR: Compare reference MSAs with alternative MSAs

Description Usage Arguments Value Author(s) References See Also

View source: R/msa_set_scoreR.R

Description

MSA reliability scores (Penn et al. 2010)

Usage

1
msa_set_scoreR(ref, alt)

Arguments

ref

An object of class DNAbin or AAbin containing aligned sequences of DNA or amino acids.

alt

single MSA or list of MSAs or path to alternative files. Single MSAs and list members should be of class DNAbin or AAbin.

Value

matrix containing following scores:

residue_pair_score: if one alternative MSA is supplied then the score is 1 if a residue pair was identically aligned as in the reference MSA and 0 otherwise. If more than one alternative MSA is used, then the average of the residue pair scores from all comparisons

Author(s)

Franz-Sebastian Krah

References

Penn et al. 2010. An alignment confidence score capturing robustness to guide tree uncertainty. Molecular Biology and Evolution 27:1759–1767.

See Also

msa_set_scoreSA


heibl/polenta documentation built on May 17, 2019, 3:22 p.m.