Aligning genomic length sequence with DECIPHER can be done using the following steps:

1. Load in the libraries and genome sequences:

library(DECIPHER)
long_seqs <- readDNAStringSet(file.path(getwd(), "datasets", "ch3", "plastid_genomes.fa"))
long_seqs

2. Prepare the sequences in a local database:

Seqs2DB(long_seqs, "XStringSet", "long_db", names(long_seqs))

3. Find the blocks of synteny:

synteny <- FindSynteny("long_db")
pairs(synteny)

This will create a dotplot of syntenic blocks.

4. Plot the syntenic blocks:

plot(synteny)

5. Now, make an actual alignment:

alignment <- AlignSynteny(synteny, "long_db")

6. And save the pairwise alignments one-by-one:

blocks <- unlist(alignment[[1]])
writeXStringSet(blocks, "genome_blocks_out.fa")