RAxML-Light statistics

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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Alexandros Stamatakis

Publication for RAxML-Light

RAxML-Light citations

 (7)
library_books

Ancient hybridization fuels rapid cichlid fish adaptive radiations

2017
Nat Commun
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 ni […]

library_books

ncRNA orthologies in the vertebrate lineage

2016
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 under […]

library_books

Whole genome sequence and analysis of the Marwari horse breed and its genetic origin

2014
BMC Genomics
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 t […]

library_books

Disk covering methods improve phylogenomic analyses

2014
BMC Genomics
PMCID: 4239662
PMID: 25572610
DOI: 10.1186/1471-2164-15-S6-S7

[…] nt] -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 supermatrix.phylip - […]

library_books

The Candidate Phylum Poribacteria by Single Cell Genomics: New Insights into Phylogeny, Cell Compartmentation, Eukaryote Like Repeat Proteins, and Other Genomic Features

2014
PLoS One
PMCID: 3909097
PMID: 24498082
DOI: 10.1371/journal.pone.0087353

[…] and modified by Douglas Jacobsen (Bioinformatics Computing Consultant, LBNL, Berkeley, USA). The script requires two input files, the alignment file as PHYLIP format and a starting tree calculated by RAxML-Light . The script workflow is briefly summarized as follows: First RAxML version 7.3.5 creates bootstrap replicates of the multiple sequence alignments and stepwise addition order parsimony tr […]

call_split

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

2013
BMC Evol Biol
PMCID: 3682911
PMID: 23627680
DOI: 10.1186/1471-2148-13-93
call_split See protocol

[…] 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 tim […]

Citations

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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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