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