[Seqinr-forum] dist.alignment gap penalty

[Stephanie Young]

Hi,
I noticed that the most recent version of dist.alignment() function doesn't produce any differences when gap = F vs when gap = T. 

Here is a toy example: 

test1 <- msa(c(test1 = "acgtg", test2 = "acgtgaa"), type = "dna", method = "ClustalOmega") |>
    msaConvert(type = "seqinr::alignment") |>
    dist.alignment(gap = F)

test2 <- msa(c(test1 = "acgtg", test2 = "acgtgaa"), type = "dna", method = "ClustalOmega") |>
    msaConvert(type = "seqinr::alignment") |>
    dist.alignment(gap = T)

> identical(test1, test2)
[1] TRUE
Is there a way to impose a gap penalty or is this function option now defunct?
Thank you,Stephanie
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/seqinr-forum/attachments/20230309/faceb128/attachment.html>