R write alignment MSA

Question

[TEman]

Hi all,

I read a clustal .aln file using the read.alignment function of the Seqinr package, modified the matrix, and now want to write the alignment object to a clustal .aln file format again. However, I do not find such a function.

Any suggestions?

[h.mon]

Suggestion 1 (faster): save alignment to fasta file with write.fasta() and convert fasta to clustal with, e.g., readseq or seqret.

Suggestion 2 (uncertain): I think the phangorn package can convert the seqinr object to a phyDat object, which could then be saved as a clustal alignment.