BioX program

By scm at Fri, Oct 13 2006 10:54pm |

I have a question about how to use ClustalW on my MacBook Pro.
I installed EBioTools on my computer, followed by BioX. Now I'm trying to align two sequences using the ClustalW option, and I'm getting an error that says:

The sequences could not be aligned with the EMBOSS command emma.

The following error message was given:
dyld: Library not loaded: /usr/X11R6/lib/libXpm.4.dylib
Referenced from: /usr/ebiotools/bin/emma
Reason: image not found

Can anyone out there take pity on me and explain what I have to do to get ClustalW to work?

Thanks so much.

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Fri, 2006-10-13 23:12 — dgohara

Re: BioX program

Hello,

A few things.

First, have you installed X11 on your system? It's an optional install and comes on your install disk (Note: If you are on Panther, you can get the pkg online from the Apple website. If you are on Tiger, you need to use the version on the install disk).

If you have X11 installed but don't see the file (check in /usr/X11R6/lib) then try downloading the Xcode package (again from the developer site) and installing the X11 SDK. I suspect however, that simply installing X11 will do the trick.

Let me know if you need more information,

Dave

Sat, 2006-10-14 00:29 — scm

Hi Dave, I accidentally

Hi Dave,

I accidentally installed X11 SDK first instead of X11, so I'm not sure which one solved the problem, but I just ran the alignment and now it works perfectly.

Thanks so much for your help!

Ruchi

Fri, 2007-01-12 21:29 — koumd

BioX couldn't write file

Just saw this comment. Very helpful. Wouldn't have left the install disc at the office. At any rate, I am also having a problem saving alignments in different formats (e.g, nexus/PAUP or phylip). When I try to do this, I get an error message that says:

Couldn't Write File
The document couldn't be written to "475-7_BF7_U_mafftalign.phy" as a Phylip sequence file by the EMBOSS seqret command.

Will installing X11 take care of this as well?