@@ -223,7 +223,7 @@ dinu_to.keep <-

             }, check.head.g, region)

         } else { # no region

             pos.to.mut <- lapply(check.head.g, function(x){

-                which(x) - 1

+                setdiff((which(x) - 1), 0)

             })

         }

@@ -238,8 +238,6 @@ dinu_to.keep <-

                     aa.tmp <- aa.to.mut.unique[i]

                     pos.to.mut.tmp <- pos.to.mut.i[aa.to.mut == aa.tmp]

-                    substr(codon.list.alt[[aa.tmp]], 3, 3)

-

                     if(!check.region){ # have region

                         pos.for.select <- intersect(which(seq.aa.i == aa.tmp),

                             which(region.i))