Dear all,

Thank you all for your comments. I've finally managed to make r8s run 
by putting the application on my directory and typing './r8s -f 
filename' directly on terminal. Since some people showed interest on 
any reply I had, here I send all the help e-mails I received.

Cheers,

Ramiro

Hi Ramiro,

I don't know if there's aproblem with your copy of r8s, but the first 
thing I do when I encounter such a problem is to update my operating 
system (MacOS 10.4.7 is out), although it seems more probable that the 
issue is text encoding. Use a text editor like TextWrangler or BBEdit 
to play around with text encoding (Macintosh, Unix, DOS). Some programs 
like DOS line breaks, for instance.

You can get both programs from http://www.barebones.com
On the main text window, click the icon to the right of the "M" icon to 
select the text encoding of your choice. See a screenshot here: 
http://www.macupdate.com/screenshot.php?id=11009

Although the program does open when you execute it in the Terminal, I 
would just navigate to the directory where both r8s and the input Nexus 
file are and do this:

$./r8s -b -f inputfile.nxs > logfile.txt

and make sure your Nexus file has all the necessary r8s commands (run 
settings, priors, etc.). Of course, you may just enter the r8s prompt 
and use the "execute" command.

Cheers,
sergios

Dr. Morales-Hojas,

I don't have experience with R8S, but I often have problems with NEXUS 
files not being recognized while trying to run phylogenetic programs 
(e.g. MrBayes) on a Mac.  One common problem is with the taxon names.  
Look in your NEXUS file as text and see if the names have single-quotes 
around them, like this: 'Drosophila'.  This was my problem with the 
NEXUS file generated by PAUP* on a Mac.  After removing these 
single-quotes (using find and remove in Word), the file was recognized 
as NEXUS.

Hope this helps.

John McCormack
UCLA

Ramiro, the first thing to check is that your files are text only; I'm 
not sure about r8s but many programs won't recognize any other format 
(e.g. .doc files from Word).

Bill

Ramiro,

r8s is a console program,
double clicking does not work well with those because when you 
double-click the program's start directory is your home directory.
Use the Terminal.app (in /Applications/Utilities) and then learn a 
couple of commands to move around
(typically you need to know: ls, cd, mv, cp [type man ls etc] or even 
better learn about the Terminal.app on 
http://www.oreillynet.com/pub/a/mac/2001/12/14/terminal_one.html.

Peter

Dear Ramiro:

I too had similar difficulties with r8s.  I got around it by opening
Terminal and then typing in:

./r8s -f filename

For some reason you must call r8s from the Terminal, not by 
double-clicking
on the executable.  Hope this helps!

Heather

Dear Ramiro,

I strngly suggest that you stop using your mouse alltogether when using
r8s and operate the program from the terminal window only. The manual
lists the necessary unix commands for running the software. However, if
you don't put the r8s program into the bin directory, you might rather 
run
it with ./r8s command.

Good luck,
Natalia

rmhojas@ibmc.up.pt