filterMSA: Filtering of the base MSA using guidance scores

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

Filtering of the base MSA using guidance scores

Description

Filtering of the base MSA using guidance scores

Usage

filterMSA(guidanceX, col.cutoff = 0.2, seq.cutoff = 0.1,
  mask.cutoff = 0.5, filter.ends = FALSE, filter.gaps = FALSE,
  na.coding = 0.5)

Arguments

guidanceX	object of class guidance
col.cutoff	numeric between 0 and 1; removes unreliable columns below the cutoff (default: 0.2); ignored if FALSE
seq.cutoff	numeric between 0 and 1; removes unreliable sequences below the cutoff (default: 0.1); ignored if FALSE
mask.cutoff	residues below the cutoff are masked ('N' for DNA, 'X' for AA; default: 0.5); ignored if FALSE
filter.ends	logical, if TRUE trim.ends (ips) is applied to the MSA
filter.gaps	logical, if TRUE trim.gabs (ips) is applied to the MSA
na.coding	value with which to replace NAs

Details

Please note that we do not recommend filtering MSAs (Tan et al. 2015). Instead the user should use the GUIDANCE column score as individual weights to each column of the alignment to RAxMLvia the –a flag (for a practical example: Krah et al. (2018)). This can be achieved by using the function scores with score = "column_raxml" and passing the score as weights to raxml. For a detailled example, see Vignette.

Value

filtered MSA of class AAbin or DNAbin

if filter.ends or filter.gaps was choosen, the adjusted

Author(s)

Franz-Sebastian Krah

References

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

Krah et al. (2018). Evolutionary dynamics of host specialization in wood-decay fungi. BMC Evolutionary Biology 18:119-132

See Also

scores

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