group_alignment: Combine two alignment results.

In Busydog1990/genepro: CProtMEDIAS: clustering of amino acid sequences encoded by gene families by MErging and DIgitizing Aligned Sequences

Combine two alignment results.

Description

Solves (Needleman-Wunsch) global alignment problems on two alignment results.

Usage

group_alignment(
  alignment1,
  alignment2,
  seqtype = "AA",
  gapOpening = -4,
  gapExtension = -1,
  substitutionMatrix = "BLOSUM62",
  standard = T,
  alignment_thres = 0
)

Arguments

alignment1	Alignment result of group1.
alignment2	Alignment result of group2.
seqtype	One of DNA, RNA and AA.
gapOpening	Numeric. The cost for opening a gap in the alignment.
gapExtension	Numeric. The incremental cost incurred along the length of the gap in the alignment.
substitutionMatrix	Substitution matrix representing the fixed substitution scores for an alignment.
standard	Logical. If TRUE, only keep the score of AA_STANDARD/DNA_BASES/RNA_BASES for protein/DNA/RNA sequences. Default:TRUE.
alignment_thres	Numeric. Remove sites with amino acid ratio lower than alignment_thres. Default:0.

Value

Combined multiple alignment results.

Busydog1990/genepro documentation built on July 20, 2023, 6:03 a.m.