RAxML pipeline

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


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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


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

 (73)
2018
PMCID: 5954287

[…] size fixed at 30, we randomly removed or duplicated chromosomes from the initial population until its size became 30. we also used the population-au as additional stopping criterion with the raxml tree being the known best ml tree and a significance level α=0.05. when there were more than one tree in the pareto optimal set, the tree with the lowest dtl-reconciliation score was returned […]

2018
PMCID: 5952958

[…] selection (guindon and gascuel 2003; darriba et al. 2012) and concatenated all msa, keeping the individual coordinate information to be used as a partition for the phylogenetic analysis. we used raxml software (option –f e) to obtain ml estimates of branch lengths and r8s software v 1.80 (sanderson 2003) to linearize the unrooted ml using the penalized likelihood algorithm. for the last […]

2018
PMCID: 5829066

[…] v2.3 (koboldt et al., 2012) and variant positions were filtered using snpfilter (version 2.2.0; see below). based on the aligned variant positions maximum-likelihood trees were calculated using raxml (version 8.2.7, model gtr gamma, 100 bootstraps; stamatakis, 2014). the genome sequence of klebsiella oxytoca konih1 (accession: cp008788) was included to root the tree displaying […]

2018
PMCID: 5771471

[…] were obtained from planmine (brandl et al., 2016). multiple sequence alignments of condensin proteins were performed using mafft (katoh et al., 2009) followed by phylogenetic tree generation using raxml (stamatakis, 2014) using the gamma wag model with 1000 bootstrap replicates. the best-scoring maximum likelihood tree was generated. the tree figure was made using geneious (kearse et al., […]

2018
PMCID: 5764404

[…] aligned using the multiple-sequence alignment method available in the mafft program, using the fft-ns-1 strategy [25]. phylogenetic inference utilized the maximum likelihood (ml) method available in raxml (v8.2.10) [26], applying the general time reversible (gtr) nucleotide substitution model with a gamma (γ) distribution of among-site rate variation. support for individual nodes was assessed […]

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.