Installing RAxML in Windows

[Courtney Cheng]

Hi!

I'm trying to install RAxML to make a gene tree, but I'm having trouble setting it up. I followed the instructions on the website:

http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html

My directory is: C:\Users\grads\Documents\RAxML\Standard-RAxML-master

When i try to type make -fMakefile.gcc i get the message "'make' is not recognized as an internal or external command, operable program or batch file." How can I fix this?

P.S. I also have Cygwin installed if that helps with anything.

Thanks!

[J.M.P. Alves]

Either you do not have the necessary tools to compile software in that computer, or it is not in a directory where Windows searches for programs. Sorry, I do not know Windows, but some googling of how to compile in Windows should help you.

Also, I remember hearing that someone here in this list has pre-compiled Windows executables recently and made them available, so if you search the list you might find that.

Good luck

J

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João Marcelo Pereira Alves (J), PhD
Genomics, Molecular Phylogeny and Evolution

[Andrej Pangerčič]

Hey,

you can install already pre-compiled raxml program. Install files are also located at github as well. That tutorial is not for windows compiling.

Regards, Andrej

[YL L]

Hello,

Actually, you don't need install it. What you need to do is just download the windows Executables edition, unpack it  and put your data files(*.phy) in the same folder. Also you need create a batch file with the notepad in your windows, type the following scripts(the red letters) into the batch file and save. Doubleclick the batch file to run it.

for standard bootstrapping: 

raxmlHPC -m GTRGAMMA -p 12345 -# 1000 -s primates.phy -n T13

raxmlHPC -m GTRGAMMA -p 12345 -b 12345 -# 1000 -s primates.phy -n T14

raxmlHPC -m GTRCAT -p 12345 -f b -t RAxML_bestTree.T13 -z RAxML_bootstrap.T14 -n T15 -o Tarsius_syrichta,Lemur_catta

for rapid bootstrapping:

raxmlHPC -f a -m GTRGAMMA -p 12345 -x 12345 -# 1000 -s primates.phy -n T20 -o Tarsius_syrichta,Lemur_catta

The latest version can be found here: 

https://github.com/stamatak/standard-RAxML/blob/master/WindowsExecutables_v8.1.20/WindowsExecutables_v8.1.20.zip

在 2014年7月21日星期一 UTC+8下午11:07:57，Courtney Cheng写道：