Shtsai at 01:28, 5 April 2026

2026-04-05T01:28:06Z

← Older revision		Revision as of 21:28, 4 April 2026
Line 1:		Line 1:
	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==
	Bioinformatics		Bioinformatics
	=== Program On ===		== Program On ==
	Sapelo2		Sapelo2
	=== Version ===		== Version ==
	1.2.2		1.2.2
	===Author / Distributor===		==Author / Distributor==
	Alexey M. Kozlov and Alexandros Stamatakis		Alexey M. Kozlov and Alexandros Stamatakis
	===Description===		==Description==
	RAxML-NG is a phylogenetic tree inference tool which 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 phylogenetic tree inference tool which 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.

	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
Line 55:		Line 55:
	Please refer to [[Running Jobs on Sapelo2]].		Please refer to [[Running Jobs on Sapelo2]].

	=== Documentation ===		== Documentation ==


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	=== Installation ===		== Installation ==

	Source code for RAxML 8.2.12 downloaded from [https://github.com/stamatak/standard-RAxML/archive/master.zip githhub] and compiled with intel-2019b compilers and intel MPI.		Source code for RAxML 8.2.12 downloaded from [https://github.com/stamatak/standard-RAxML/archive/master.zip githhub] and compiled with intel-2019b compilers and intel MPI.

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Jordan: There was still a reference to using an "MPI version" even though we don't have an MPI version of this software installed.

2024-10-22T14:00:27Z

There was still a reference to using an "MPI version" even though we don't have an MPI version of this software installed.

← Older revision		Revision as of 10:00, 22 October 2024
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	Example of shell script to run ~~the MPI version~~ in the batch queue, using ~~32 MPI processes~~:		Example of shell script to run in the batch queue, using 8 cores on a single node:

	<div class="gscript2">		<div class="gscript2">

Jordan at 14:34, 3 July 2024

2024-07-03T14:34:41Z

← Older revision		Revision as of 10:34, 3 July 2024
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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml RAxML-NG/1.2.2-GCC-12.2.0<br> \		ml RAxML-NG/1.2.2-GCC-12.2.0<br>
	~~raxml-ng~~ raxml-ng --all --msa testAA.fa --model LG+G8+F --tree pars{10} --bs-trees 200 --threads 8<br>		raxml-ng --all --msa testAA.fa --model LG+G8+F --tree pars{10} --bs-trees 200 --threads 8<br>
	</div>		</div>

Jordan: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.2.2 ===Author / Distributor=== Alexey M. Kozlov and Alexandros Stamatakis ===Description=== RAxML-NG is a phylogenetic tree inference tool which 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 qu..."

2024-07-01T15:39:08Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.2.2 ===Author / Distributor=== Alexey M. Kozlov and Alexandros Stamatakis ===Description=== RAxML-NG is a phylogenetic tree inference tool which 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 qu..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===
Bioinformatics
=== Program On ===
Sapelo2
=== Version ===
1.2.2
===Author / Distributor===
Alexey M. Kozlov and Alexandros Stamatakis
===Description===
RAxML-NG is a phylogenetic tree inference tool which 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.

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''RAxML-NG'''

To use RaxML-NG, please first load the module with
<pre class="gscript">
module load RAxML-NG/1.2.2-GCC-12.2.0
</pre>

Keep in mind that because this version doesn't use MPI, the job cannot be run on multiple nodes, thought it can use multiple threads on a single node.

Example of shell script to run the MPI version in the batch queue, using 32 MPI processes:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_RAxML-NG 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --cpus-per-task=8 #this needs to be the same as the '--threads' option below! 
<nowiki>#</nowiki>SBATCH --mem=64GB 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=RAxML-NG.%j.out 
<nowiki>#</nowiki>SBATCH --error=RAxML-NG.%j.err 

cd $SLURM_SUBMIT_DIR 
ml RAxML-NG/1.2.2-GCC-12.2.0 \
raxml-ng raxml-ng --all --msa testAA.fa --model LG+G8+F --tree pars{10} --bs-trees 200 --threads 8 
</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running Jobs on Sapelo2]].

=== Documentation ===

<pre class="gcommand">

ml RAxML-NG/1.2.2-GCC-12.2.0
raxml-ng --help

RAxML-NG v. 1.2.2-master released on 30.04.2024 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

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 (default: 10 parsimony + 10 random starting trees)
--bootstrap bootstrapping (default: use bootstopping to auto-detect #replicates)
--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
--bsmsa generate bootstrap replicate MSAs
--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
--rfdist compute pair-wise Robinson-Foulds (RF) distances between trees
--consense [ STRICT | MR | MR<n> | MRE ] build strict, majority-rule (MR) or extended MR (MRE) consensus tree (default: MR)
eg: --consense MR75 --tree bsrep.nw
--ancestral ancestral state reconstruction at all inner nodes
--sitelh print per-site log-likelihood values

Command shortcuts (mutually exclusive):
--search1 Alias for: --search --tree rand{1}
--loglh Alias for: --evaluate --opt-model off --opt-branches off --nofiles --log result
--rf Alias for: --rfdist --nofiles --log result

Input and output options:
--tree rand{N} | pars{N} | FILE starting tree: rand(om), pars(imony) or user-specified (newick file)
N = number of trees (default: rand{10},pars{10})
--msa FILE alignment file
--msa-format VALUE alignment file format: FASTA, PHYLIP, CATG or AUTO-detect (default)
--data-type VALUE data type: DNA, AA, BIN(ary) or AUTO-detect (default)
--tree-constraint FILE constraint tree
--prefix STRING prefix for output files (default: MSA file name)
--log VALUE log verbosity: ERROR,WARNING,RESULT,INFO,PROGRESS,DEBUG (default: PROGRESS)
--redo overwrite existing result files and ignore checkpoints (default: OFF)
--nofiles do not create any output files, print results to the terminal only
--precision VALUE number of decimal places to print (default: 6)
--outgroup o1,o2,..,oN comma-separated list of outgroup taxon names (it's just a drawing option!)
--site-weights FILE file with MSA column weights (positive integers only!)

General options:
--seed VALUE seed for pseudo-random number generator (default: current time)
--pat-comp on | off alignment pattern compression (default: ON)
--tip-inner on | off tip-inner case optimization (default: OFF)
--site-repeats on | off use site repeats optimization, 10%-60% faster than tip-inner (default: ON)
--threads VALUE number of parallel threads to use (default: 1)
--workers VALUE number of tree searches to run in parallel (default: 1)
--simd none | sse3 | avx | avx2 vector instruction set to use (default: auto-detect).
--rate-scalers on | off use individual CLV scalers for each rate category (default: ON for >2000 taxa)
--force [ <CHECKS> ] disable safety checks (please think twice!)

Model options:
--model <name>+G[n]+<Freqs> | FILE model specification OR partition file
--brlen linked | scaled | unlinked branch length linkage between partitions (default: scaled)
--blmin VALUE minimum branch length (default: 1e-6)
--blmax VALUE maximum branch length (default: 100)
--blopt nr_fast | nr_safe branch length optimization method (default: nr_fast)
nr_oldfast | nr_oldsafe
--opt-model on | off ML optimization of all model parameters (default: ON)
--opt-branches on | off ML optimization of all branch lengths (default: ON)
--prob-msa on | off use probabilistic alignment (works with CATG and VCF)
--lh-epsilon VALUE log-likelihood epsilon for optimization/tree search (default: 0.1)

Topology search options:
--spr-radius VALUE SPR re-insertion radius for fast iterations (default: AUTO)
--spr-cutoff VALUE | off relative LH cutoff for descending into subtrees (default: 1.0)
--lh-epsilon-triplet VALUE log-likelihood epsilon for branch length triplet optimization (default: 1000)

Bootstrapping options:
--bs-trees VALUE number of bootstraps replicates
--bs-trees autoMRE{N} use MRE-based bootstrap convergence criterion, up to N replicates (default: 1000)
--bs-trees FILE Newick file containing set of bootstrap replicate trees (with --support)
--bs-cutoff VALUE cutoff threshold for the MRE-based bootstopping criteria (default: 0.03)
--bs-metric fbp | tbe branch support metric: fbp = Felsenstein bootstrap (default), tbe = transfer distance
--bs-write-msa on | off write all bootstrap alignments (default: OFF)

EXAMPLES:
1. Perform tree inference on DNA alignment
(10 random + 10 parsimony starting trees, general time-reversible model, ML estimate of substitution rates and
nucleotide frequencies, discrete GAMMA model of rate heterogeneity with 4 categories):

./raxml-ng --msa testDNA.fa --model GTR+G

2. Perform an all-in-one analysis (ML tree search + non-parametric bootstrap)
(10 randomized parsimony starting trees, fixed empirical substitution matrix (LG),
empirical aminoacid frequencies from alignment, 8 discrete GAMMA categories,
200 bootstrap replicates):

./raxml-ng --all --msa testAA.fa --model LG+G8+F --tree pars{10} --bs-trees 200

3. Optimize branch lengths and free model parameters on a fixed topology
(using multiple partitions with proportional branch lengths)

./raxml-ng --evaluate --msa testAA.fa --model partitions.txt --tree test.tree --brlen scaled
</pre>

=== Installation ===

Source code for RAxML 8.2.12 downloaded from [https://github.com/stamatak/standard-RAxML/archive/master.zip githhub] and compiled with intel-2019b compilers and intel MPI.

=== System ===
64-bit Linux

RAxML-NG-Sapelo2 - Revision history

Shtsai at 01:28, 5 April 2026

Jordan: There was still a reference to using an "MPI version" even though we don't have an MPI version of this software installed.

Jordan at 14:34, 3 July 2024