How to install phyml on mac

[Johanna Ledwaba]

Hi everyone,

I am new on MAC OS X so i need help in installing PhyML on mac. I have downloaded PhyML 3.1 what is the next step? May someone take me through this step by step...

Regards,

Johanna.

[Quentin CAUDRON]

Hi Johanna,

There is a web interface, if you prefer not to install anything. However, if you prefer to have it running locally, you have a few options. By far the simplest is to simply run the compiled binary for Mac, which you can find in this zip archive :

http://www.atgc-montpellier.fr/download/binaries/phyml/PhyML-3.1.zip

Inside that archive is a file called PhyML-3.1_macOS-MountainLion. This thing's ready to go - just call it from the command line, either with arguments or in interactive mode. That is, in a terminal and in this directory :

./PhyML-3.1_macOS-MountainLion 

will run PhyML for "interactive" use. If you want to throw a PHYLIP file at it with some arguments, it's similar :

./PhyML-3.1_macOS-MountainLion -d nt -m GTR -i myalignment.phy 

for example, will build a tree from the nucleotide sequences in myalignment.phy, using the GTR model. For a list of command line arguments, check the README.

For easy access, you might want to move the file and rename it :

mv PhyML-3.1_macOS-MountainLion /usr/loca/bin/phyml

Then, you can call the phyml command from anywhere in your system.

The other option is to compile it from source. Instructions are in the README, and it goes fairly smoothly with the usual ./configure; make; make install. You can compile with MPI, if you've got it installed, to allow parallel bootstrapping for speed.

Hope that helps.

Quentin