RAxML-NG

RAxML-NG on ACCESS

RAxML-NG is a phylogenetic tree inference tool that uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. RAxML-NG is a successor of RAxML (Stamatakis 2014) and leverages the highly optimized likelihood computation implemented in libpll (Flouri et al. 2014).

RAxML-NG offers improvements in speed, flexibility and user-friendliness over the previous RAxML versions. It also implements some of the features previously available in ExaML (Kozlov et al. 2015), including checkpointing and efficient load balancing for partitioned alignments (Kobert et al. 2014).

RAxML-NG is currently under active development, and the mid-term goal is to have most functionality of RAxML 8.x covered. You can see some of the planned features here.

The RAXML-NG user group is here

The table below shows the example files form a RAxML-NG run.:

Input File Names Sample File from a Test
input file infile.txt
partition file part.txt
   
Sample Output File Type File Name
best tree infile.txt.raxml.bestTree
log file infile.txt.raxml.log
Trees file infile.txt.raxml.mlTrees
.rba file infile.txt.raxml.rba
Starting trees file infile.txt.raxml.startTree

If you use RAxML-NG, please cite:

Alexey M. Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, and Alexandros Stamatakis (2019) RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35 (21), 4453-4455 doi.org/10.1093/bioinformatics/btz305

If there is a tool or a feature you need, let us know.

hummingbird in flight

Get 1000 Hours free

On the UCSD Supercomputer

Start Your Trial