[Seqinr-forum] dist.alignment gap penalty

[PENEL SIMON]

Hi Stephanie

the new release is available on RForge

https://r-forge.r-project.org/R/?group_id=220

install.packages("seqinr", repos="http://R-Forge.R-project.org")

and on its way to the CRAN

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

> test2
          test1
test2 0.5345225

all the best

Simon




________________________________________
De : Seqinr-forum <seqinr-forum-bounces at lists.r-forge.r-project.org> de la part de PENEL SIMON <Simon.Penel at univ-lyon1.fr>
Envoyé : jeudi 16 mars 2023 15:41
À : Stephanie Young; seqinr-forum at lists.r-forge.r-project.org
Objet : Re: [Seqinr-forum] dist.alignment gap penalty

Hi Stephanie
it seems that the Rforge encounter some problems.
We are planning to use github or gitlab instead.
In the meantime, I will send the package to the CRAN and I can send you the sources of the package if you wish

all the best

Simon


________________________________________
De : PENEL SIMON
Envoyé : mercredi 15 mars 2023 16:49
À : Stephanie Young; seqinr-forum at lists.r-forge.r-project.org
Cc : LOBRY RAYMOND
Objet : RE: [Seqinr-forum] dist.alignment gap penalty

Hi Stephanie,

I submitted a new version of seqinr to the forge.
https://r-forge.r-project.org/R/?group_id=220
It is currently building,  when it  is ready  I will let you know.

all the best,

Simon


________________________________________
De : PENEL SIMON
Envoyé : mercredi 15 mars 2023 10:35
À : Stephanie Young; seqinr-forum at lists.r-forge.r-project.org
Cc : LOBRY RAYMOND
Objet : RE: [Seqinr-forum] dist.alignment gap penalty

Hi Stephanie,

thanks for spotting this
The  gap penalty option is indeed disabled for dna sequences,  I will change this and let you now as soon as this is done,

all the best


________________________________________
De : Seqinr-forum <seqinr-forum-bounces at lists.r-forge.r-project.org> de la part de Stephanie Young <stefunnie_young at yahoo.com>
Envoyé : jeudi 9 mars 2023 05:28
À : seqinr-forum at lists.r-forge.r-project.org
Objet : [Seqinr-forum] dist.alignment gap penalty

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
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