Primarily I have attempted to install the MrBayes program. I have entered the MrBayes web site (http://mrbayes.sourceforge.net/download.php) and then I have downloaded it with the link for Macintosh(64bit), but I didn't succeed in running it. I installed the file but it doesn't include any running file (it only includes documentation and examples).
I haven't succeeded in installing BioEdit in the same way either.
Is there anyone who can help me? (I use an iMac- OS X 10.8.2)
First, BioEdit is a program available on Windows platform only. If you want to run it on your Mac, you will need to install a desktop virtualization software such as VMware fusion. This will allow you to install Windows on your Mac and any Windows applications you need – including BioEdit.
Second, make sure you use the following link to install MrBayes (http://sourceforge.net/projects/mrbayes/files/latest/download?source=files). This is a package and it should work quite seamlessly on your Mac.
Instead of BioEdit, try Se-Al. It is a mac based program and allows you do much of the same edits as BioEdit. There are a few tricks, you may need to drag the fasta file into the program the first time, always save when the sequence is DNA, you can toggle between amino acid and codon views but will lose data if you save in those modes.
http://tree.bio.ed.ac.uk/software/seal/
Consider using Mr Bayes at the CIPRES gateway instead of downloading to you computer.
http://www.phylo.org/portal2/login!input.action
Dear Labrie
thank you for your interest
for MrBayes, I have tried several times using your link, but I can't run. dot coming typical file symbol (file to run). there are only documentation and examples files. I didn't understand anything.
for BioEdit, also I will try as you say.
Dear Sherman-Broyles
thank you for your interest
http://tree.bio.ed.ac.uk/software/seal/ I have entered to this link. I have downloaded ''Se-Al v2.0.dmgDisk Image for Mac OS X (PPC or Intel)'' but this file didn't run
could you check again?
Is CIPRES' program free?
I have used another virtual machine on my Mac, VirtualBox , easier to work with than VMare Fusion. You can then easily install BioEdit there too. Try.
Dear Omer,
I tried both links/softwares you are having difficulty with and both worked on my computer. For MrBays, there is a small delay and then the file is downloaded. It's a pkg file. The only thing you need to do is to double click on it and it's going to run and install the software.
yes I downloaded a pkg file. and than I ran this file, set up successfully on mac . A file (MrBayes 3.2 ) was existed in Applications. it has only 2 file (documentation and examples). not exist running file of this program. I have searched everywhere, but have not found.
here is my problem.
MrBayes is a command line application. Here is what's written after the installation is completed:
++++++++++++++++++
MrBayes has been installed to "/usr/local/bin". You can run MrBayes from any Terminal window by typing "mb".
Example files and documentation for MrBayes have been installed in the MrBayes3.2 directory in the Applications folder. Refer to the manual or the program web site for additional information about MrBayes.
If you have an NVIDIA graphics card (GPU), MrBayes can make use of it through BEAGLE to significantly accelerate analyses. To enable the use of your NVIDIA GPU, please download and install the latest NVIDIA CUDA drivers for Mac OS X from nvidia.com:
NVIDIA CUDA drivers for Mac
+++++++++++++++++++
MrBayes manual is very complete and it's a very good tool.
Eventually, I have solved to this problem. Simon, thank you for your helps.
I didn't read this part. I thought like windows. I waited a separate running file.
Now, I am running by using terminal.
at the same time, I have download latest NVIDIA CUDA drivers, but nothing happened.
Hi, Simon:
I have installed Mrbayes 3.2.2 with GPU. I checked when I type ./mb, Mrbayes > showbeagle
Resouce 1: Quadro 5000 Desc: Global Memory (MB): 2559 | Clock speed ( Ghz): 1:03 | Number of Cores 352.
I run one big file with 329 sample with 15000 bp sequences. when I exec test.nex, it will takes 792 hour.
Should I use MPI to run with GPU? Could you share the command line running mrbayes with MPI in GPU? I hope that I can at least use 256 cores.
Thank you very much,
All the best,
Runhua
I had a similar problem after switching to mac os. I have now found a good replacement for BioEdit. It´s called AliView and it can do multiple sequence alignments, and much more, is light weight and a "sidescroller" - maybe take a look at it if it can do what you need:
http://www.ormbunkar.se/aliview/#top
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