**0**wrote:

Hello guys, I am final year bioinformatics student, doing internship at the moment. So i am sorry for my noobiness in advance.

Here is what i was told to do, i have 100+ fasta files, and need to run pairwise sequence alignment with each other and save the outcome. Here is what i did and the errors i am getting.

`library(seqinr)`

`setwd("C:\\Users\\Celik\\Downloads\\fasta\\R_deneme")`

files = list.files(pattern="*.fasta")

seq = lapply(files, read.fasta)

library(Biostrings)

`pws.alignments <- sapply(1:(length(seq)-1), function(ind)`

`{`

sapply((ind+1):length(seq), function(sec.ind)

{

return(pairwiseAlignment(seq[[ind]], seq[[sec.ind]]))

})

})

Error in (function (classes, fdef, mtable) :

unable to find an inherited method for function ‘seqtype’ for signature ‘"SeqFastadna"’

I appreciate your help, thanks.

**3.5k**• written 4.9 years ago by mastercod3r •

**0**

maybe try

`readDNAStringSet`

instead`read.fasta`

?2.8k