RAxML statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RAxML
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Tool usage distribution map

This map represents all the scientific publications referring to RAxML per scientific context
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Associated diseases

This word cloud represents RAxML usage per disease context
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Popular tool citations

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Protocols

RAxML specifications

Information


Unique identifier OMICS_02242
Name RAxML
Alternative names Randomized Axelerated Maximum Likelihood, RAxML-VI-HPC, RAxML-III
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA,PHYLIP,NEWICK
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 8.2.11
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Alexandros Stamatakis

Additional information


https://github.com/stamatak/standard-RAxML/wiki https://embnet.vital-it.ch/raxml-bb/

Information


Unique identifier OMICS_02242
Name RAxML
Alternative names Randomized Axelerated Maximum Likelihood, RAxML-VI-HPC, RAxML-III
Interface Web user interface
Restrictions to use None
Input data A sequence alignment
Input format PHYLIP+NEWICK
Computer skills Basic
Stability Stable
Maintained No

Download


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Documentation


Maintainer


This tool is not maintained anymore.

Additional information


https://github.com/stamatak/standard-RAxML/wiki https://embnet.vital-it.ch/raxml-bb/

Publications for Randomized Axelerated Maximum Likelihood

RAxML citations

 (5165)
call_split

The first isolate of Candida auris in China: clinical and biological aspects

2018
PMCID: 5959928
PMID: 29777096
DOI: 10.1038/s41426-018-0095-0
call_split See protocol

[…] The internal transcribed sequences (ITS) of C. auris BJCA001 and previously reported isolates were aligned using mafft v7.015b. The Maximum- Likelihood phylogenetic tree was generated using RAxML v7.3.2. The General Time Reversible (GTR) model and Gamma distribution with Invariant sites (G + I) were adopted. Schizosaccharomyces pombe strain ATCC 38366 was used as an outgroup, whereas Can […]

library_books

An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots

2018
PMCID: 5953950
PMID: 29765033
DOI: 10.1038/s41426-018-0089-y

[…] Z_LZRE00000000)), generated in Geneious v10. This core genome contig was also used to re-map the reads of the poorly assembled genomes (with <20× average coverage) from this study. A mid-point rooted RaXML phylogenetic tree with 500 bootstraps and GTR CAT I model was constructed using multiple sequence MAFFT alignment of the 271 kbp core genome of 27 C. psittaci strains, as implemented in Geneious […]

library_books

Chitinase genes (CHIAs) provide genomic footprints of a post Cretaceous dietary radiation in placental mammals

2018
Sci Adv
PMCID: 5955627
PMID: 29774238
DOI: 10.1126/sciadv.aar6478

[…] CHIA1 sequences, all CHIA2 sequences, etc.), and then each subclade alignment was aligned successively using the Geneious Translation align tool implementing the MUSCLE algorithm. We then performed a RAxML analysis on this finalized alignment (data set S1) in CIPRES using the same parameters (fig. S1). […]

call_split

Endocytosis mediated siderophore uptake as a strategy for Fe acquisition in diatoms

2018
Sci Adv
PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536
call_split See protocol

[…] ed using Geneious and trimmed at the N terminus to the first methionine present and at the C terminus to the last residue of the protein (with 70% identity). Trees were inferred using the MrBayes and RAxML programs inbuilt into the CIPRES webserver (table S1). A Bayesian tree was inferred using three substitution models (GTR, Jones, and WAG), a minimum of 600,000 generations, and an initial burn-i […]

library_books

Multiple origins of green blood in New Guinea lizards

2018
Sci Adv
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] gene trees (tables S2 and S3) (). In addition, modeling for incomplete lineage sorting using a coalescent approach (ASTRAL) yielded topologies that were concordant with our unpartitioned ML approach (RAxML), indicating that our data were robust to problems of incomplete lineage sorting. Despite strong support for four green-blood lineages (), the number of evolutionary transitions between red and […]

library_books

The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites

2018
Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] e used PartitionFinder v2, with the settings: (i) unlink branch lengths and (ii) use the corrected Akaike information criterion (AICc) for model selection. ML and BI analyses were performed using the RAxML web-server (http://embnet.vital-it.ch/raxml-bb/index.php ) and MrBayes v3.2.4 under the best substitution models and partition scheme identified (Supplementary Table ). Bayesian analyses were ru […]


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RAxML institution(s)
Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
RAxML funding source(s)
Supported by the Heidelberg Institute for Theoretical Studies.

RAxML review

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Erica Souza

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Desktop
Software based on command lines, it is not friendly to use if you don't understand clearly how command line work. Although the initial difficult to the language the software have a interesting algorithm that produce a confident Maximum likelihood tree. In addition, the users need to search friendly protocol to use it because it official manual is not so clearly.