[Bio-Linux] Mapmaker on Bio-linux 4?

[H.Evans at liverpool.ac.uk]

thanks, its working fine now!

Helen.




Quoting Dan Swan <bioinformatics.lists at gmail.com>:

> On 4/5/06, H.Evans at liverpool.ac.uk <H.Evans at liverpool.ac.uk> wrote:
> > hello,
> >
> > does anyone know if there is a problem with the mrbayes program on
> biolinux?
> >
> > i cant get the program to execute the primates.nex file which is used in
> the
> > tutorial.  i have moved it into the same directory as the software but it
> still
> > says:
> >
> > MrBayes > execute primates.nex
> >
> >    Executing file "primates.nex"
> >    Could not open file "primates.nex"
> >    Error in command "Execute"
>
> Hi Helen,
>
> you need to point MrBayes to the file - I assume you have run 'mb'
> from your home directory.
>
> try:
>
> execute /usr/local/bioinf/mrbayes/mrbayes-3.1.1/samplefiles/primates.nex
>
> you will see:
>
>    Executing file
> "/usr/local/bioinf/mrbayes/mrbayes-3.1.1/samplefiles/primates.nex"
>    UNIX line termination
>    Longest line length = 915
>    Parsing file
>    Expecting NEXUS formatted file
>    Reading data block
>       Allocated matrix
>       Matrix has 12 taxa and 898 characters
>       Data is Dna
>       Data matrix is not interleaved
>       Gaps coded as -
>       Setting default partition (does not divide up characters).
>       Taxon  1 -> Tarsius_syrichta
>       Taxon  2 -> Lemur_catta
>       Taxon  3 -> Homo_sapiens
>       Taxon  4 -> Pan
>       Taxon  5 -> Gorilla
>       Taxon  6 -> Pongo
>       Taxon  7 -> Hylobates
>       Taxon  8 -> Macaca_fuscata
>       Taxon  9 -> M_mulatta
>       Taxon 10 -> M_fascicularis
>       Taxon 11 -> M_sylvanus
>       Taxon 12 -> Saimiri_sciureus
>       Setting output file names to
>
"/usr/local/bioinf/mrbayes/mrbayes-3.1.1/samplefiles/primates.nex.<run<i>.p/run<i>.t>"
>       Successfully read matrix
>    Exiting data block
>    Reached end of file
>
> regards,
>
> Dan
>
> --
> Senior Research Associate, Bioinformatics Support Unit,
> Institute for Cell and Molecular Biosciences,
> Faculty of Medical Sciences, Framlington Place,
> University of Newcastle upon Tyne,
> Newcastle, NE2 4HH
> Tel: +44 (0)191 222 7253  (Leech offices: Rooms M.2046/M.2046A)
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>
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