In article 11466 at emba.uvm.edu, brianf at med.uvm.edu (Brian Foley) writes:
> The documentation says that the output created by PILEUP
>(the pileup.msf file) can be used as input to PLOTSIMILARITY.
>> However, this is not working for me. PLOTSIM says it cannot
>read pileup.msf. The documantation also says that all the sequences
>have to be the same length, and my PILEUP was of sequences of
>various lengths, gaps were introduced. Could this be the problem?
>If so, how does one plot the similarity of proteins that have
>udergone deletions/insertions during evolution?
>>
Brian,
You must designate which sequences in the file pileup.msf are to be used by PLOTSIMILARITY. You can select all of the sequences in the msf file by giving
pileup.msf{*}
the {*} (left-curly-q asterisk right-curly-q) designates all of the sequences in your file pileup.msf
good luck
Mike Neubauer
