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RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs

https://doi.org/10.1007/11535294_25
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/bf01734359openalex-snapshot
Evolutionary trees from DNA sequences: A maximum likelihood approach
inferredcites →https://doi.org/10.1016/0025-5564(86)90161-6openalex-snapshot
The computational complexity of inferring rooted phylogenies by parsimony
inferredcites →https://doi.org/10.1016/s0304-3975(98)00342-9openalex-snapshot
The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs
inferredcites →https://doi.org/10.1080/10635150290102366openalex-snapshot
Potential Applications and Pitfalls of Bayesian Inference of Phylogeny
inferredcites →https://doi.org/10.1080/10635150390235520openalex-snapshot
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/10.1.41openalex-snapshot
fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/18.3.502openalex-snapshot
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
inferredcites →https://doi.org/10.1093/bioinformatics/bti100openalex-snapshot
DPRml: distributed phylogeny reconstruction by maximum likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/bti191openalex-snapshot
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
inferredcites →https://doi.org/10.1093/molbev/msh176openalex-snapshot
IQPNNI: Moving Fast Through Tree Space and Stopping in Time
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025664openalex-snapshot
Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025808openalex-snapshot
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
inferredcites →https://doi.org/10.1109/bibe.2003.1188932openalex-snapshot
An investigation of phylogenetic likelihood methods
inferredcites →https://doi.org/10.1109/bibe.2004.1317396openalex-snapshot
Phylogenetic reconstruction from arbitrary gene-order data
inferredcites →https://doi.org/10.1109/csb.2003.1227337openalex-snapshot
Efficient reconstruction of phylogenetic networks with constrained recombination
inferredcites →https://doi.org/10.1109/ipdps.2005.90openalex-snapshot
An Efficient Program for Phylogenetic Inference Using Simulated Annealing
inferredcites →https://doi.org/10.1117/12.434868openalex-snapshot
Industrial applications of high-performance computing for phylogeny reconstruction
inferredcites →https://doi.org/10.1126/science.1065889openalex-snapshot
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
inferredcites →https://doi.org/10.1142/9789814447362_0053openalex-snapshot
SCALING OF ACCURACY IN EXTREMELY LARGE PHYLOGENETIC TREES
inferredcites →https://doi.org/10.1142/s0219720004000521openalex-snapshot
OPTIMAL, EFFICIENT RECONSTRUCTION OF PHYLOGENETIC NETWORKS WITH CONSTRAINED RECOMBINATION
inferredcites →https://doi.org/10.1145/582034.582054openalex-snapshot
Parallel implementation and performance of fastDNAml

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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First discovery of a new species of Newmanella Ross, 1969 (Balanomorpha: Tetraclitidae) in the western Pacific, with a note on the new status of Neonrosella Jones, 2010
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Lentibacillus garicola sp. nov., isolated from myeolchi-aekjeot, a Korean fermented anchovy sauce
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Phylogenetic position of the enigmatic myxomycete genus Kelleromyxa revealed by SSU rDNA sequences
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New records of the rare North American endemic Chara brittonii (Characeae), with comments on its distribution
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Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae)
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A Multigene Analysis of Corallomyxa tenera sp. nov. Suggests its Membership in a Clade that Includes Gromia, Haplosporidia and Foraminifera
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Multigene Evidence for the Placement of a Heterotrophic Amoeboid Lineage Leukarachnion sp. among Photosynthetic Stramenopiles
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Phylogenomic workflow for uncultivable microbial eukaryotes using single-cell RNA sequencing − A case study with planktonic ciliates (Ciliophora, Oligotrichea)
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Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions
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Genome-wide genetic variation coupled with demographic and ecological niche modeling of the dusky-footed woodrat (Neotoma fuscipes) reveal patterns of deep divergence and widespread Holocene expansion across northern California
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Contrasting and complex evolutionary histories within the terapontid grunter genus Hephaestus revealed by nuclear and mitochondrial genes
inferred← citeshttps://doi.org/10.1071/mf20167openalex-snapshot
Genome-wide phylogenetic study of Percomorpha providing robust support for previous molecular classification
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Reciprocal monophyly of Craspedia and Pycnosorus (Asteraceae, Gnaphalieae) and the problems of using ribosomal DNA at the lowest taxonomic levels
inferred← citeshttps://doi.org/10.1080/10635150802429642openalex-snapshot
A Rapid Bootstrap Algorithm for the RAxML Web Servers
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Analysis of plant gene family heat shock protein 100 (HSP100) and its orthologs in Eukarya reveals sites of divergent evolution and insights into endosymbiotic origins of chloroplasts
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New insights into the molecular phylogeny of the swimming crabs of the genera Portunus Weber, 1795 and Achelous De Haan, 1833 (Brachyura: Portunidae) of the Americas
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ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning
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PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes
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Barcoding Bamboozled by Bacteria: Convergence to Metazoan Mitochondrial Primer Targets by Marine Microbes
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Taxon-Rich Phylogenomic Analyses Resolve the Eukaryotic Tree of Life and Reveal the Power of Subsampling by Sites
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Molecular basis for three-dimensional elaboration of theAquilegiapetal spur
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Garicola koreensis gen. nov., sp. nov., isolated from saeu-jeot, traditional Korean fermented shrimp
inferred← citeshttps://doi.org/10.1099/ijs.0.000133openalex-snapshot
Aliiglaciecola aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium, isolated from a sea-tidal flat and emended description of the genus Aliiglaciecola Jean et al. 2013
inferred← citeshttps://doi.org/10.1099/ijs.0.000199openalex-snapshot
Aestuariicella hydrocarbonica gen. nov., sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from a sea tidal flat
inferred← citeshttps://doi.org/10.1099/ijs.0.000381openalex-snapshot
Celeribacter naphthalenivorans sp. nov., a naphthalene-degrading bacterium from tidal flat sediment
inferred← citeshttps://doi.org/10.1099/ijs.0.028332-0openalex-snapshot
Citreicella aestuarii sp. nov., isolated from a tidal flat
inferred← citeshttps://doi.org/10.1099/ijs.0.029173-0openalex-snapshot
Luteimonas lutimaris sp. nov., isolated from a tidal flat
inferred← citeshttps://doi.org/10.1099/ijs.0.032367-0openalex-snapshot
Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi
inferred← citeshttps://doi.org/10.1099/ijs.0.037846-0openalex-snapshot
Aestuariibaculum suncheonense gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a tidal flat and emended descriptions of the genera Gaetbulibacter and Tamlana
inferred← citeshttps://doi.org/10.1099/ijs.0.038943-0openalex-snapshot
Kordiimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat
inferred← citeshttps://doi.org/10.1099/ijs.0.039024-0openalex-snapshot
Altererythrobacter gangjinensis sp. nov., a marine bacterium isolated from a tidal flat
inferred← citeshttps://doi.org/10.1099/ijs.0.040683-0openalex-snapshot
Arenibacter hampyeongensis sp. nov., a marine bacterium isolated from a tidal flat
inferred← citeshttps://doi.org/10.1099/ijs.0.042606-0openalex-snapshot
Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus sp. nov., isolated from marine environments
inferred← citeshttps://doi.org/10.1099/ijs.0.048389-0openalex-snapshot
Defluviimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat, and emended description of the genus Defluviimonas Foesel et al. 2011
inferred← citeshttps://doi.org/10.1099/ijs.0.048561-0openalex-snapshot
Aquamicrobium aestuarii sp. nov., a marine bacterium isolated from a tidal flat
inferred← citeshttps://doi.org/10.1099/ijs.0.048694-0openalex-snapshot
Gramella aestuarii sp. nov., isolated from a tidal flat, and emended description of Gramella echinicola
inferred← citeshttps://doi.org/10.1099/ijs.0.049197-0openalex-snapshot
Brevibacterium jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood
inferred← citeshttps://doi.org/10.1099/ijs.0.050054-0openalex-snapshot
Maribacter aestuarii sp. nov., isolated from tidal flat sediment, and an emended description of the genus Maribacter
inferred← citeshttps://doi.org/10.1099/ijs.0.050807-0openalex-snapshot
Roseovarius lutimaris sp. nov., isolated from a marine tidal flat
inferred← citeshttps://doi.org/10.1099/ijs.0.055178-0openalex-snapshot
Shewanella aestuarii sp. nov., a marine bacterium isolated from a tidal flat
inferred← citeshttps://doi.org/10.1099/ijs.0.056861-0openalex-snapshot
Photobacterium aestuarii sp. nov., a marine bacterium isolated from a tidal flat
inferred← citeshttps://doi.org/10.1099/ijs.0.058396-0openalex-snapshot
Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter
inferred← citeshttps://doi.org/10.1099/ijs.0.062042-0openalex-snapshot
Salimicrobium jeotgali sp. nov., isolated from salted, fermented seafood
inferred← citeshttps://doi.org/10.1099/ijs.0.063669-0openalex-snapshot
Flavihumibacter solisilvae sp. nov., isolated from forest soil
inferred← citeshttps://doi.org/10.1099/ijs.0.068593-0openalex-snapshot
Zhongshania aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from marine sediment, and transfer of Spongiibacter borealis Jang et al. 2011 to the genus Zhongshania as Zhongshania borealis comb. nov.
inferred← citeshttps://doi.org/10.1099/ijs.0.068684-0openalex-snapshot
Litoribaculum gwangyangense gen. nov., sp. nov., isolated from a sea-tidal flat sediment
inferred← citeshttps://doi.org/10.1099/ijsem.0.000561openalex-snapshot
Confluentimicrobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from sea-tidal-flat sediment, and emended description of the genus Confluentimicrobium Park et al. 2015
inferred← citeshttps://doi.org/10.1099/ijsem.0.000563openalex-snapshot
Alteromonas naphthalenivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from tidal-flat sediment
inferred← citeshttps://doi.org/10.1099/ijsem.0.000784openalex-snapshot
Halomonas garicola sp. nov., isolated from saeu-jeot, a Korean salted and fermented shrimp sauce
inferred← citeshttps://doi.org/10.1099/ijsem.0.000884openalex-snapshot
Lysobacter aestuarii sp. nov., isolated from estuary sediment
inferred← citeshttps://doi.org/10.1099/ijsem.0.000913openalex-snapshot
Arenimonas aestuarii sp. nov., isolated from estuary sediment
inferred← citeshttps://doi.org/10.1099/ijsem.0.000942openalex-snapshot
Maribacter lutimaris sp. nov., isolated from marine sediment
inferred← citeshttps://doi.org/10.1099/ijsem.0.001438openalex-snapshot
Piscinibacter defluvii sp. nov., isolated from a sewage treatment plant, and emended description of the genus Piscinibacter Stackebrandt et al. 2009
inferred← citeshttps://doi.org/10.1099/ijsem.0.001630openalex-snapshot
Roseovarius confluentis sp. nov., isolated from estuary sediment
inferred← citeshttps://doi.org/10.1099/ijsem.0.001711openalex-snapshot
Algoriphagus aestuariicola sp. nov., isolated from estuary sediment
inferred← citeshttps://doi.org/10.1099/mic.0.047779-0openalex-snapshot
Identification of a novel subgroup of uncultured gammaproteobacterial glycogen-accumulating organisms in enhanced biological phosphorus removal sludge
inferred← citeshttps://doi.org/10.1099/vir.0.037937-0openalex-snapshot
Raspberry leaf blotch virus, a putative new member of the genus Emaravirus, encodes a novel genomic RNA
inferred← citeshttps://doi.org/10.1101/2020.01.09.899906openalex-snapshot
ModelTeller: model selection for optimal phylogenetic reconstruction using machine learning
inferred← citeshttps://doi.org/10.1109/aiccsa.2010.5586973openalex-snapshot
Evolutionary placement of short sequence reads on multi-core architectures
inferred← citeshttps://doi.org/10.1109/cibcb.2015.7300275openalex-snapshot
Taenia biomolecular phylogeny and the impact of mitochondrial genes on this latter
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Load Balance in the Phylogenetic Likelihood Kernel
inferred← citeshttps://doi.org/10.1109/ipdps.2007.370267openalex-snapshot
RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine
inferred← citeshttps://doi.org/10.1109/ipdps.2013.70openalex-snapshot
Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference
inferred← citeshttps://doi.org/10.1109/ipdpsw.2010.5470900openalex-snapshot
Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code
inferred← citeshttps://doi.org/10.1109/ispa.2012.105openalex-snapshot
Evaluating the Performance of a Parallel Multiobjective Artificial Bee Colony Algorithm for Inferring Phylogenies on Multicore Architectures
inferred← citeshttps://doi.org/10.1109/tpds.2014.2355205openalex-snapshot
Multi-Threaded Hierarchical Clustering by Parallel Nearest-Neighbor Chaining
inferred← citeshttps://doi.org/10.1111/cla.12007openalex-snapshot
Phylogenetic relationships of the A ustralasian shrubby everlastings O zothamnus and C assinia ( A steraceae: A steroideae: G naphalieae)
inferred← citeshttps://doi.org/10.1111/j.1365-2699.2012.02742.xopenalex-snapshot
Phylogeography of the cold‐water barnacle Chthamalus challengeri in the north‐western Pacific: effect of past population expansion and contemporary gene flow
inferred← citeshttps://doi.org/10.1111/j.1420-9101.2010.02018.xopenalex-snapshot
Conspicuousness is correlated with toxicity in marine opisthobranchs
inferred← citeshttps://doi.org/10.1111/j.1439-0485.2012.00520.xopenalex-snapshot
Sympatric seagrass shrimp show similar structure and selection along the seashore: a comparison of two cryptic Phycomenes zostericola lineages
inferred← citeshttps://doi.org/10.1111/j.1469-8137.2011.03744.xopenalex-snapshot
Petal‐specific subfunctionalization of an APETALA3 paralog in the Ranunculales and its implications for petal evolution
inferred← citeshttps://doi.org/10.1111/j.1529-8817.2012.01127.xopenalex-snapshot
SYSTEMATICS OF THE GENUS ZYGNEMA (ZYGNEMATOPHYCEAE, CHAROPHYTA) FROM CALIFORNIAN WATERSHEDS1
inferred← citeshttps://doi.org/10.1111/j.1550-7408.2009.00445.xopenalex-snapshot
A Description of a New “Amoebozoan” Isolated from the American Lobster, Homarus americanus
inferred← citeshttps://doi.org/10.1111/jpy.12229openalex-snapshot
Phylogenetic position of Z ygogonium ericetorum ( Z ygnematophyceae, C harophyta) from a high alpine habitat and ultrastructural characterization of unusual aplanospores
inferred← citeshttps://doi.org/10.1145/1229428.1229445openalex-snapshot
Dynamic multigrain parallelization on the cell broadband engine
inferred← citeshttps://doi.org/10.1145/1362622.1362628openalex-snapshot
Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L
inferred← citeshttps://doi.org/10.1145/1645164.1645178openalex-snapshot
Scientific workflow design with data assembly lines
inferred← citeshttps://doi.org/10.1155/2008/395908openalex-snapshot
Large-Scale Phylogenetic Analysis on Current HPC Architectures
inferred← citeshttps://doi.org/10.11606/t.41.2012.tde-18012013-160032openalex-snapshot
Tempo e espaço na evolução de Cnidaria Medusozoa - estudos filogeográficos com ênfase em populações do Atlântico Sul-ocidental, e datações da origem das principais linhagens dos cnidários
inferred← citeshttps://doi.org/10.11646/zootaxa.2787.1.1openalex-snapshot
Cryptic diversity of the semi-terrestrial amphipod Platorchestia japonica (Tattersall, 1922) (Amphipoda: Talitrida: Talitridae) in Japan and Taiwan, with description of a new species
inferred← citeshttps://doi.org/10.1186/1471-2148-10-165openalex-snapshot
Evolution of nectarivory in phyllostomid bats (Phyllostomidae Gray, 1825, Chiroptera: Mammalia)
inferred← citeshttps://doi.org/10.1186/s12862-016-0719-8openalex-snapshot
Founder events and pre-glacial divergences shape the genetic structure of European Collembola species
inferred← citeshttps://doi.org/10.12705/644.6openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pgen.1005534openalex-snapshot
Insect Resistance to Bacillus thuringiensis Toxin Cry2Ab Is Conferred by Mutations in an ABC Transporter Subfamily A Protein
inferred← citeshttps://doi.org/10.1371/journal.pone.0029696openalex-snapshot
Broad Phylogenomic Sampling and the Sister Lineage of Land Plants
inferred← citeshttps://doi.org/10.1371/journal.pone.0057592openalex-snapshot
Host-Specific Phenotypic Plasticity of the Turtle Barnacle Chelonibia testudinaria: A Widespread Generalist Rather than a Specialist
inferred← citeshttps://doi.org/10.1371/journal.pone.0062566openalex-snapshot
Phylogeny, Floral Evolution, and Inter-Island Dispersal in Hawaiian Clermontia (Campanulaceae) Based on ISSR Variation and Plastid Spacer Sequences
inferred← citeshttps://doi.org/10.1600/036364410x539899openalex-snapshot
Taxonomic Revision of the Endangered Hawaiian Red-flowered Sandalwoods (Santalum) and Discovery of an Ancient Hybrid Species
inferred← citeshttps://doi.org/10.1600/036364411x604958openalex-snapshot
A New Amazonian Section of Protium (Burseraceae) including both Edaphic Specialist and Generalist Taxa. Studies in Neotropical Burseraceae XVI.
inferred← citeshttps://doi.org/10.1894/cmt-03.1openalex-snapshot
Conservation Genetics of Cyprinid Fishes (Genus Dionda) in Southwestern North America. II. Expansion of the Known Range of the Manantial Roundnose Minnow, Dionda argentosa
inferred← citeshttps://doi.org/10.2174/157489306777011888openalex-snapshot
Accomplishments and Challenges in High Performance Computing for Computational Biology
inferred← citeshttps://doi.org/10.22507/rli.v14n2a11openalex-snapshot
Análisis de haplotipos de la tortuga cabezona Caretta caretta (Testudines: Cheloniidae) en dos playas del Caribe colombiano
inferred← citeshttps://doi.org/10.2478/prge-2012-0002openalex-snapshot
Gene discovery from a pilot study of the transcriptomes from three diverse microbial eukaryotes: Corallomyxa tenera, Chilodonella uncinata, and Subulatomonas tetraspora
inferred← citeshttps://doi.org/10.3417/2010131openalex-snapshot
The MADS-Box Gene Family of the Basal Eudicot and HybridAquilegia coerulea‘Origami' (Ranunculaceae)1
inferred← citeshttps://doi.org/10.34719/rjbz6161openalex-snapshot
The Role Of Software Engineering In Bioinformatics
inferred← citeshttps://doi.org/10.3732/ajb.1000059openalex-snapshot
Phylogeny, adaptive radiation, and historical biogeography in Bromeliaceae: Insights from an eight‐locus plastid phylogeny
inferred← citeshttps://doi.org/10.3732/ajb.1700172openalex-snapshot
First discovery of the charophycean green alga Lychnothamnus barbatus (Charophyceae) extant in the New World
inferred← citeshttps://doi.org/10.3767/003158509x479487openalex-snapshot
Unravelling Mycosphaerella: do you believe in genera?
inferred← citeshttps://doi.org/10.4236/jsea.2022.157016openalex-snapshot
Generic Tabu Search
inferred← citeshttps://doi.org/10.4236/ojapps.2022.126069openalex-snapshot
Generic Simulated Annealing
inferred← citeshttps://doi.org/10.6119/jmst-013-1220-7openalex-snapshot
Genetic Diversity of Filamentous Cyanobacteria from Shore Regions of Okinawa
inferred← citeshttps://doi.org/10.70675/77cd418cz1b0cz4dd0z9d8czf009e0fd8fafopenalex-snapshot
Investigating the Impact of Insertion Sequences on the Evolution of Prokaryotic Genomes
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