> ## this script trims flanking regions from the alignments
> 
> library(shipunov)
package 'shipunov', version 1.3-1

> ## empty list with names per fragment
> dna <- structure(vector("list", 2), names=c("abcd", "efgh"))

> ## go to directoty with alignments
> setwd("30_alignments")

> for (f in names(dna)) {
+  dna[[f]] <- Read.fasta(paste0(f, ".fasta"))
+  bb <- do.call(rbind, strsplit(dna[[f]]$sequence, split="")) # split string sequences into nucleotide sequences
+  dd <- apply(bb, 2, function(.x) sum(.x == "-")/nrow(bb)) # count gaps
+  ee <- runmed(dd, 3) < 0.5 # trimming criterion: three subsequent sequence positions have more then 50% of non-gaps
+  left <- min(which(ee == TRUE)) # calculate left trimming position
+  right <- max(which(ee == TRUE)) # calculate right trimming position
+  ff <- bb[,left:right] # trim!
+  dna[[f]]$sequence <- apply(ff, 1, paste, collapse="") # join nucleotides into strings again
+  Write.fasta(dna[[f]], file=paste0("../31_alignments_trimmed/", f, ".fasta"))
+ }