new file mode 100644

@@ -0,0 +1,28 @@

+msaConvert <- function(x, type=c("seqinr::alignment",

+                                 "bios2mds::align"))

+{

+    type <- match.arg(type)

+

+    if (!is(x, "MultipleAlignment"))

+        stop("x must be a 'MultipleAlignment' object")

+

+    x <- as.character(unmasked(x))

+

+    if (type == "seqinr::alignment")

+    {

+        out <- list(nb=length(x),

+                    nam=names(x),

+                    seq=unname(x),

+                    com=NA)

+

+        class(out) <- "alignment"

+    }

+    else if (type == "bios2mds::align")

+    {

+        out <- .Call("SplitCharVector2List", x)

+        names(out) <- names(x)

+        class(out) <- "align"

+    }

+

+    out

+}