scores: Score Calculation

In heibl/polenta: Multiple Sequence Alignment with PASTA and GUIDANCE

Description

Calculate additional scores based on residue pair score.

Usage

scores(polenta, score = c("alignment", "column", "residue", "sequence"),
  na.rm = TRUE)

Arguments

polenta	object of class polenta
score	A character string indicating a type of score, currently available "column", "residue", "alignment", "sequence", "all".
na.rm	Logical, indicating if NA should be removed.

Details

The score 'column' is the GUIDANCE column score which is the mean of the residue pair residue score across columns. The score 'alignment' is the mean across the residue pair residue scores. The score 'sequence' is the mean of the residue pair score across rows (sequences). The score 'residue' is the mean score across the residue pairs with that residue (residue pair score).

The GUIDANCE column score can be utilized to weight characters in RAxML (flag -a). Simple removal of sites from the MSA should be done with cautions (Tan et al. 2015).

Value

data.frame or list of data.frames with scores

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.

Tan et al. (2015). Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference. Systematic biology 64:778–791.

See Also

filterMSA

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