[Seqinr-forum] bug in dist,alignment

[Jean Lobry]

Yes, but you need an external program to make the
alignment, see for instance ?reverse.align

Le 10/02/2020 à 17:22, Russell J Gray a écrit :
> I see.
> 
> Is there any way to get distances for sequences without the same number 
> of characters for all sequences?
> 
> Best,
> 
> -RG
> 
> 
> 
> *--*
> *Russell J. Gray*
> Wildlife Ecology & Conservation Consultant
> 
> 0934581341 | rgrayherpetology at gmail.com <mailto:rgrayherpetology at gmail.com>
> 
> https://www.rjgrayecology.com/
> 
> 705 alligator ranch rd. New Smyrna Beach, FL, USA. 32168
> 
> 
> 
> 
> On Monday, February 10, 2020, 09:29:54 p.m. GMT+7, Jean Lobry 
> <jean.lobry at univ-lyon1.fr> wrote:
> 
> 
> A problem here is that the file "Amanita.txt" does
> not contain an alignment since the number of characters
> is not the same for all sequences :
> 
>  > library(seqinr)
>  > dna <- read.alignment("Amanita.txt", format = "fasta")
>  > unlist(lapply(dna$seq, nchar))
>    [1] 626 625 639 687 646 676 670 517 497 770 720 713 730 563 540
>  >
> 
> Le 10/02/2020 à 05:56, Russell J Gray a écrit :
>  > Hi there,
>  >
>  > I'm trying to use the seqinr package for some ITS sequence analysis and
>  > when I run the first basic functions of the package it automatically
>  > crashes R. I've attached my FASTA text file, and have copied my code
>  > here....
>  > Once you run the line "*D <- dist.alignment(dna, matrix =
>  > "similarity")*" if you try to view the dna data, or if R autocompletes a
>  > function, or you try to do anything further, R runs the "Fatal Error"
>  > window and says it cannot connect to the server.
>  >
>  >
>  > *library(seqinr)*
>  > *library(adegenet)*
>  > *library(ape)*
>  > *library(ggtree)*
>  > *
>  > *
>  > *
>  > *
>  > *dna <- read.alignment("Amanita.txt", format = "fasta")*
>  > *D <- dist.alignment(dna, matrix = "similarity")*
>  > *
>  > *
>  >
>  > Any help is appreciated!
>  >
>  > Best regards
>  >
>  > -RG
>  >
>  >
>  > *--*
>  > *Russell J. Gray*
>  > Wildlife Ecology & Conservation Consultant
>  >
>  > 0934581341 | rgrayherpetology at gmail.com 
> <mailto:rgrayherpetology at gmail.com> <mailto:rgrayherpetology at gmail.com 
> <mailto:rgrayherpetology at gmail.com>>
> 
>  >
>  > https://www.rjgrayecology.com/
>  >
>  > 705 alligator ranch rd. New Smyrna Beach, FL, USA. 32168
> 
>  >
>  >
>  >
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