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Tutorial
RAxML-NG replaces standard RAxML as well as the corresponding supercomputer version ExaML. So RAxML-NG is one single code base that scales from the laptop to the supercomputer. RAxML-NG does not (yet) support all options of standard RAxML, only the most important and frequently used ones. Some options are now implemented as stand-alone tools, e.g. phylogenetic placement (EPA).
This tutorial is based on RAxML-NG practical taught by Alexandros Stamatakis at COME 2018. It will cover most common use cases, for information on advanced usage see next section.
Before you start:
- Download and install RAxML-NG (instructions)
- Download a toy dataset:
If you run RAxML-NG executable without parameters, it will show quick usage help:
RAxML-NG v. 0.7.0git BETA released on 31.10.2018 by The Exelixis Lab.
Authors: Alexey Kozlov, Alexandros Stamatakis, Diego Darriba, Tomas Flouri, Benoit Morel.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
WARNING: This is a BETA release, please use at your own risk!
Usage: raxml-ng [OPTIONS]
Commands (mutually exclusive):
--help display help information
--version display version information
--evaluate evaluate the likelihood of a tree (with model+brlen optimization)
--search ML tree search.
--bootstrap bootstrapping
--all all-in-one (ML search + bootstrapping).
--support compute bipartition support for a given reference tree (e.g., best ML tree)
and a set of replicate trees (e.g., from a bootstrap analysis)
--bsconverge test for bootstrapping convergence using autoMRE criterion
--terrace check whether a tree lies on a phylogenetic terrace
--check check alignment correctness and remove empty columns/rows
--parse parse alignment, compress patterns and create binary MSA file
--start generate parsimony/random starting trees and exit
--loglh compute the likelihood of a fixed tree (no model/brlen optimization)
Input and output options:
[...]
More comprehensive documentation is available in GitHub wiki. Further information and benchmarks can be found in biorxiv preprint and in Chapter 4 of Alexey's PhD thesis.
If you cannot find an answer to your question in the above sources, or if you think you found a bug, please contact us via RAxML google group.
- Please use search function before posting, since many questions have been answered before.
- Please use google group and not personal e-mail for asking questions about RAxML-NG. This will save everybody's time: you might get help sooner from other Exelixis lab members or your fellow users. And whoever might encounter the same problem in the future will benefit from the answer.
Before, we get started, let's first check that the MSA can actually be read and doesn't contain sites with only undetermined characters or sequences with undetermined characters or duplicate taxon names, etc. etc.
raxml-ng --check --msa test.fa --model GTR+G --prefix T1
Doing this check before getting started is super-important as more than 50% of all failed raxml runs are due to tree or MSA format errors!!!!
We will always also use --prefix to avoid over-writing previous output files!
Now let's infer a tree under GTR+GAMMA with default parameters:
raxml-ng --msa test.txt --model GTR+G --prefix T2