Learning RAxML

[Rishi]

Hi,

I have recently become interested in bioinformatics and I thought that RAxML would be a good place to start. I was wondering if there are any resources that example the biology and algorithm behind RAxML to its fullest extent. Any information would be very much appreciated. Thank you in advance.

[Alexandros Stamatakis]

Please see:

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

which contains links to the manual, a step by step hands on example
etc., for the algorithms you will need to read the RAxML papers,

alexis

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[lucas...@h-its.org]

Hi Rishi,

as a general introduction to phylogeny inference, you may want to have a look at "Computational Molecular Evolution" by Ziheng Yang.

Lucas

[Rishi]

Hi Alexis,

Where can I go to find the RAxML papers? I have found some papers, but I am not sure if they are the same set of papers you are referring to.

Regards,

Rishi

[Alexandros Stamatakis]

check the four main papers:

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with
thousands of taxa and mixed models

A rapid bootstrap algorithm for the RAxML web servers

RAxML version 8: a tool for phylogenetic analysis and post-analysis of
large phylogenies

RAxML-III: a fast program for maximum likelihood-based inference of
large phylogenetic trees

alexis