From jai_mohan2003 at yahoo.com  Fri Apr 14 05:53:46 2006
From: jai_mohan2003 at yahoo.com (jaimohan sm)
Date: Fri, 14 Apr 2006 02:53:46 -0700 (PDT)
Subject: [Bio-linux-list] Hi to all Bio Linux users
Message-ID: <20060414095346.49293.qmail@web31112.mail.mud.yahoo.com>

I am jaimohan sm and i am new to this list.
  i am expecting this biolinux mialing list be very useful for me.
  thanks
  bye
  jaimohan sm

		
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From H.Evans at liverpool.ac.uk  Wed Apr  5 09:12:04 2006
From: H.Evans at liverpool.ac.uk (H.Evans at liverpool.ac.uk)
Date: Wed, 05 Apr 2006 14:12:04 +0100
Subject: [Bio-Linux] Mapmaker on Bio-linux 4?
In-Reply-To: <s40d5706.059@wpo.nerc.ac.uk>
References: <s40d5706.059@wpo.nerc.ac.uk>
Message-ID: <1144242724.4433c22475524@webmaila.liv.ac.uk>

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"

helen.



From bioinformatics.lists at gmail.com  Wed Apr  5 12:33:34 2006
From: bioinformatics.lists at gmail.com (Dan Swan)
Date: Wed, 5 Apr 2006 17:33:34 +0100
Subject: [Bio-Linux] Mapmaker on Bio-linux 4?
In-Reply-To: <1144242724.4433c22475524@webmaila.liv.ac.uk>
References: <s40d5706.059@wpo.nerc.ac.uk>
	<1144242724.4433c22475524@webmaila.liv.ac.uk>
Message-ID: <d606310d0604050933y484ffb47l2b2adc0d049b2976@mail.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)
Tel: +44 (0)191  246 4833 (Devonshire offices: Rooms G.25/G.26)
Website: http://bioinf.ncl.ac.uk/support/



From H.Evans at liverpool.ac.uk  Thu Apr  6 09:47:31 2006
From: H.Evans at liverpool.ac.uk (H.Evans at liverpool.ac.uk)
Date: Thu, 06 Apr 2006 14:47:31 +0100
Subject: [Bio-Linux] Mapmaker on Bio-linux 4?
In-Reply-To: <d606310d0604050933y484ffb47l2b2adc0d049b2976@mail.gmail.com>
References: <s40d5706.059@wpo.nerc.ac.uk>
	<1144242724.4433c22475524@webmaila.liv.ac.uk>
	<d606310d0604050933y484ffb47l2b2adc0d049b2976@mail.gmail.com>
Message-ID: <1144331251.44351bf3c0c46@webmaila.liv.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)
> Tel: +44 (0)191  246 4833 (Devonshire offices: Rooms G.25/G.26)
> Website: http://bioinf.ncl.ac.uk/support/
>
> _______________________________________________
> Bio-linux mailing list
> Bio-linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
>