filterMSA: Filtering of the base MSA using polenta scores

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

Description

Filtering of the base MSA using polenta scores

Usage

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

Arguments

polenta	object of class polenta
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
column_score	logical, if TRUE column score (e.g. for RAxML: flag -a) is in the output
flag_a	character specifying a path. If path is supplied function writes the filtered MSA into a fasta file. Additionally the function produces a file with the column score ready for RAxML input (flag -a)
na.coding	XXX.

Value

masked MSA of class AAbin or DNAbin

column_score is optional

Author(s)

Franz-Sebastian Krah

See Also

scores

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