RAxML-Light statistics

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RAxML-Light specifications

Information


Unique identifier OMICS_08026
Name RAxML-Light
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MPI
Computer skills Advanced
Version 1.0.8
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Alexandros Stamatakis <>

Publication for RAxML-Light

RAxML-Light in publications

 (5)
PMCID: 5309898
PMID: 28186104
DOI: 10.1038/ncomms14363

[…] to get a dataset of the original size. the maximum likelihood tree was then inferred for each resampled dataset with examl (ref. ) using a gtrgamma model of rate heterogeneity, as recommended in the raxml-light manual. we calculated bootstrap support values based on these 100 topologies with raxml (ref. ). the nuclear and mitochondrial trees were rooted with the reference genome of oreochromis […]

PMCID: 4792531
PMID: 26980512
DOI: 10.1093/database/bav127

[…] of input sequence) to build genomic trees with the aforementioned strategy in a reasonable amount of time. for these families we build fast trees using fasttree2 () with options -nt -quiet -nopr and raxml-light (version 1.0.6) () in combination with parsimonator v.1.0.2 (http://sco.h-its.org/exelixis/software.html), a lightweight and fast implementation for building starting trees for raxml […]

PMCID: 4290615
PMID: 25521865
DOI: 10.1186/1471-2164-15-S9-S4

[…] 100 25). after the filtering and pruning process, 25,854 snps remained and were used for the phylogenetic analysis. raxml version 7.28-alpha [] was used to generate the parsimony starting trees, and raxml-light version 1.0.9 [] was used to carry out tree inference with the gtrgamma model of nucleotide substitutions. a total of 100 bootstrap trees were generated for each phylogeny. the resulting […]

PMCID: 4239662
PMID: 25572610
DOI: 10.1186/1471-2164-15-S6-S7

[…] -n [output name] -n 200 -p [random seed number] -b [random seed number] , concatenation: for the concatenated analysis, we computed a parsimony starting tree using raxml version 7.3.5, and then ran raxml-light version 1.0.6. we used the following commands:, raxmlhpc-sse3 -y -s supermatrix.phylip -m gtrgamma -n [output name] -p [random seed number] , raxmllight-pthreads -t 4 -s […]

PMCID: 3682911
PMID: 23627680
DOI: 10.1186/1471-2148-13-93

[…] shimodaira-hasegawa-like (shl) implementation of the approximate likelihood-ratio test (alrt; []). this involved a two-stage strategy. we first performed initial ml tree- inference using the program raxml-light v1.0.7 [], a modification of the original raxml algorithm []. this program uses the gtrcat strategy for all genes and partitions, a high-speed approximation of the gtr+γ model (general […]


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RAxML-Light institution(s)
The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Blackrim Lab, Department of Ecology and Evolutionary Biology, University of Michigan, MI, USA
RAxML-Light funding source(s)
Supported, in part, by German Science Foundation (DFG) grants STA 860/2; and STA 860/3, the NSF (National Science Foundation) iPlant collaborative, and via institutional funding from the Heidelberg Institute of Theoretical Studies.

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