Dear all, I have recently tried the package bgafun and am having problems with the sequence file format. I have a file in CLUSTAL format (*.aln). I have checked the read.alignment details and the file fulfills the criteria. I am using the commands: >LDH <- read.alignment(file = "clustalw.aln", format = "clustal") >class(LDH) [1] "alignment" this command: >LDH.amino = convert_aln_amino(LDH) is slow, and echoes the content of the file back to me. Scrolling through the screen, I can see a couple of error messages: [4871] "-" "-" "-" "-" [1] "Error for position " "1673" "in " "-" "-" [6] "-" "-" "-" "-" "-" The aligned file (*.aln) looks like this: CLUSTAL W (1.81) multiple sequence alignment MDH9402143 ------------------------------------------------------------ MDH1933634 ------------------------------------------------------------ MDH4407328 ------------------------------------------------------------ ... MDH9402143 -----MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGG--- GSPRRLGLLGSPL MDH1933634 -----MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGG--- GSPRRLGLLGSPL MDH4407328 -----MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGG--- GSPRRLGLLGSPL I have saved the output directly from CLUSTAL in .aln format, and it is accepted by other sequence programs, e.g. MEGA. If anyone can shed any light onto what I am doing wrong with the alignment, I would greatly appreciate it. With thanks for your time, Lavinia Gordon. ------------------------------------------------------- Bioinformatics Department Rm SW916, 9th Floor Murdoch Children's Research Institute Royal Children's Hospital Flemington Road, Parkville Victoria 3052 Australia Tel: (+613) 8341 6221 -------------------------------------------------------