msa_set_score: Compare reference MSA with alternative MSA(s)

In FranzKrah/rGUIDANCE: rGUIDANCE – alignment confidence score computation in R

Compare reference MSA with alternative MSA(s)

Description

MSA reliability scores (Penn et al. 2010)

Usage

msa_set_score(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.

Details

In principle this can also be done via AlignStat::compare_alignments, but slower.

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.

FranzKrah/rGUIDANCE documentation built on Jan. 27, 2024, 10:42 a.m.