This software for phylogenetic analysis is from Alexandros Stamatakis- 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 for students (possibly without administrator access to their computers) to learn about RAxML as well as macs and UNIX. Contact me if you have suggestions.
1. Choose and 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
Further comments and suggestions:
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/biology/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/biology/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
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.Download the source from https://github.com/stamatak/standard-RAxML and read the readme file for suggestions.
Last login: Wed Jun 15 18:13:08 powerbook-g4-12:~ home$ ftp http://www.sfu.ca/biology/staff/dc/raxml/raxml/raxml.zip Requesting http://www.sfu.ca/biology/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:
# 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!
ftp http://wwwkramer.in.tum.de/exelixis/countSource728.php raxmlHPC ftp http://wwwkramer.in.tum.de/exelixis/software/RAxML-7.2.8-ALPHA.tar.bz2
If you get the message-Launch of "raxml" failed: the PowerPC architecture is no longer supported.
Try using RAxML version 7.4.2 for AVX