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RAxML in five steps
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Installing and running RAxML on a Mac in less than a minute

This software for phylogenetic analysis is from Alexandros Stamatakis (Exelixis Lab)- I have not included instructions as you need to read his manual and other help included on his RAxML software page. The purpose of this page is to get you running RAxML as quickly as possible (even if you don't have administrator access to your computer). Please tell me if you use this page or have suggestions for improving it.

View our online database of Fossil Fungi palynomorphs, from Kalgutkar & Jansonius (2000), published in Palynology.

1. Download the most recent version that will run on your mac:

2. Double click raxml.zip to unzip raxml folder (unless your browser expanded it)
3. Open the Terminal program (in the Applications/Utilities folder)
4. cd into the raxml folder (you may want to move the raxml folder to your home folder- or see suggestions below)
5. ./raxml (in terminal, enter the name of the program with ./ in front plus the raxml commands- see manual or readme for one quick example). ./raxml -v will give you the version and this will do a quick run: 

./raxml -p 100 -s raxmlinput.txt -n test.out -m PROTCATWAG
Threads error? Try 
./raxml -p 100 -s raxmlinput.txt -n test.out -m PROTCATWAG  -T 2

Further comments and suggestions:

  • So you can see what is happening, open a finder window (of the 'home') alongside the terminal window. You will see raxml.zip appear, then the folder raxml, and then you can open the raxml directory to see the files inside it.
  • In a finder window you can copy a file name and then when you paste it in the Terminal window the complete path of the file (/Users/carmean/Documents/raxml/angiosperms.nex) will be included.
  • You can easily get to any directory in terminal by typing cd (and then space) and then dragging the finder window to the terminal window and letting go. Alternatively you can open any directory (folder) within terminal by typing "open /path/" e.g. "open /Users/carmean/Documents/raxml/"

    Compile RAxML on a Mac

    You can compile RAxML on your Mac if you have installed Xcode (free from Apple) and downloaded the RAxML source code (look for 'Download ZIP'). Read the 'readme' file- use the command 'make -f path/to/Downloads/Makefile. I added the extension .gcc to the Makefile for AVX supplied in the folder 'standard-RAxML-master'. 

    make -f /Users/USER-ACCOUNT/Downloads/standard-RAxML-master/Makefile.AVX.PTHREADS.mac.gcc

    I compiled RAxML-VI-HPC (v2.2.3) on a powerPC G4 Macintosh Powerbook with OS X 10.4. This executable runs on a G4, a G5 and an intel iMac. I compiled the others on more recent macs. On Snow Leopard you only need to download the source files, unzip, and in terminal run the command 

    make -f Makefile.gcc

    in order to compile RAxML. More recent versions were compiled from downloaded, unmodified code using the command 

     make -f Makefile.SSE3.PTHREADS.gcc

    of whatever was suggested by the readme text. James Munro wrote detailed instructions for compiling and using RAxML on older Macs.

    Tanay Bose wrote that RaxML 7.4.2 gives some error message while trying to bootstap certain files. In the old command line we never had to put both "-#" and "-p" but now for ML analysis we need to put values for pseudoreplicates and parsimony search separately. e.g.: 

    ./raxmlHPC-AVX -f d -# 50 -p 50 -s primates.phy -n primatestest.out -m GTRGAMMA

    Alternate Instructions (direct from terminal) Open the Terminal program (in the Applications/Utilities folder) and in a new terminal window copy and paste the command lines separately (e.g. "open raxml.zip" is a terminal command, and you must wait for it to complete- you will see a small window open & close briefly). 

    
ftp http://www.sfu.ca/biology2/staff/dc/raxml/raxml/raxml.zip  
open raxml.zip
cd raxml
ls    (is it contained within a subdirectory?  if so, cd into that)
./raxml  (provide options)

    Instructions for Intel macs-

    
ftp http://www.sfu.ca/biology2/staff/dc/raxml/raxml/raxmlHPC.zip  
open raxmlHPC.zip
cd raxmlHPC
ls    (is it contained within a subdirectory?  if so, cd into that)
./raxmlHPC -s raxmlinput.txt -n test.out -m PROTCATWAG
 


    Last login: Wed Jun 15 18:13:08 
powerbook-g4-12:~ home$ ftp http://www.sfu.ca/biology2/staff/dc/raxml/raxml/raxml.zip
Requesting http://www.sfu.ca/biology2/staff/dc/raxml/raxml/raxml.zip
100% |*************************************|   189 KB    2.19 MB/s    00:00 ETA
194079 bytes retrieved in 00:00 (1.28 MB/s)
powerbook-g4:~ home$ open raxml.zip
powerbook-g4:~ home$ cd raxml
powerbook-g4:raxml home$ ./raxml -s raxmlinput.txt -n test.out -m PROTCATWAG

RAxML rapid hill-climbing mode for AA data

Executing 1 inference on the original alignment using a distinct randomized MP tree

    Image of Terminal Window (UNIX):

    # Further comments and suggestions:

    # So you can see what is happening, open a finder window (of the 'home') alongside the terminal window. You will see raxml.zip appear, then the folder raxml, and then you can open the raxml directory to see the files inside it.

    # In a finder window you can copy a file name and then when you paste it in the Terminal window the complete path of the file (/Users/carmean/Documents/raxml/angiosperms.nex) will be included.

    # You can easily get to any directory in terminal by typing cd (and then space) and then dragging the finder window to the terminal window and letting go. Alternatively you can open any directory (folder) within terminal by typing "open /path/" e.g. "open /Users/carmean/Documents/raxml/"

    # The raxml executable will not process a file or do anything useful except open the terminal if you double click it- you must use it within the terminal window.

    Test command line: ./raxml -s raxmlinput.txt -n test.out -m PROTCATWAG

    Not clear? Ask me. Suggestions please!

    If you get the error message- 

    Launch of "raxml" failed: the PowerPC architecture is no longer supported.

    Try using RAxML version 7.4.2 for AVX

    If you get the error message- 

    Illegal instruction

    You may have an older processor, and either need to use an earlier version of RAxML or use a newer computer.