[Seqinr-forum] bug in dist,alignment

[Russell J Gray]

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
 |
| 
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>
> 
> https://www.rjgrayecology.com/
> 
> 705 alligator ranch rd. New Smyrna Beach, FL, USA. 32168
> 
> 
> 
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