<html><head></head><body><div class="yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:13px;"><div dir="ltr" data-setdir="false"><div><div dir="ltr" data-setdir="false">Hi,</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">I noticed that the most recent version of dist.alignment() function doesn't produce any differences when gap = F vs when gap = T. <br></div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Here is a toy example: <br></div></div><div><br></div><div dir="ltr" data-setdir="false"><div>test1 <- msa(c(test1 = "acgtg", test2 = "acgtgaa"), type = "dna", method = "ClustalOmega") |><br> msaConvert(type = "seqinr::alignment") |><br> dist.alignment(gap = F)<br><br>test2 <- msa(c(test1 = "acgtg", test2 = "acgtgaa"), type = "dna", method = "ClustalOmega") |><br> msaConvert(type = "seqinr::alignment") |><br> dist.alignment(gap = T)<br><br>> identical(test1, test2)<br>[1] TRUE</div><div><br></div><div dir="ltr" data-setdir="false">Is there a way to impose a gap penalty or is this function option now defunct?</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Thank you,</div><div dir="ltr" data-setdir="false">Stephanie<br></div></div></div></div></body></html>