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

[Dan Swan]

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

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