seqdiff — seqdiff • ggmsa

calculate difference of two aligned sequences

seqdiff(fasta, reference = 1)

Arguments

fasta	fasta file
reference	which sequence serve as reference, 1 or 2

Value

SeqDiff object

Author

guangchuang yu

Examples

fas <- list.files(system.file("extdata", "GVariation", package="ggmsa"),
                  pattern="fas", full.names=TRUE)
seqdiff(fas[1], reference=1)
#> sequence differences of Mont and CF_YL21 
#> 1181 sites differ:
#>   A   C   G   T 
#> 286 315 301 279