Relevant bibliographies by topics / RaxML

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'RaxML'

Author: Grafiati
Published: 4 June 2021
Last updated: 4 February 2022

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Journal articles on the topic "RaxML"

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Kozlov, Alexey M., Diego Darriba, Tomáš Flouri, Benoit Morel, and Alexandros Stamatakis. "RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference." Bioinformatics 35, no. 21 (May 9, 2019): 4453–55. http://dx.doi.org/10.1093/bioinformatics/btz305.

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Abstract Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets. Results We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric. Availability and implementation The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng. RAxML-NG web service (maintained by Vital-IT) is available at https://raxml-ng.vital-it.ch/. Supplementary information Supplementary data are available at Bioinformatics online.
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Silvestro, Daniele, and Ingo Michalak. "raxmlGUI: a graphical front-end for RAxML." Organisms Diversity & Evolution 12, no. 4 (September 1, 2011): 335–37. http://dx.doi.org/10.1007/s13127-011-0056-0.

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Lutteropp, Sarah, Alexey M. Kozlov, and Alexandros Stamatakis. "A fast and memory-efficient implementation of the transfer bootstrap." Bioinformatics 36, no. 7 (November 22, 2019): 2280–81. http://dx.doi.org/10.1093/bioinformatics/btz874.

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Abstract Motivation Recently, Lemoine et al. suggested the transfer bootstrap expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support for taxon-rich datasets. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Results We developed a fast and memory-efficient TBE implementation. We improve upon the original algorithm by Lemoine et al. via several algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10× to 40× memory savings compared with booster. Availability and implementation Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallel version that also computes additional TBE-related statistics is available at: https://github.com/lutteropp/raxml-ng/tree/tbe. Supplementary information Supplementary data are available at Bioinformatics online.
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Stamatakis, A., A. J. Aberer, C. Goll, S. A. Smith, S. A. Berger, and F. Izquierdo-Carrasco. "RAxML-Light: a tool for computing terabyte phylogenies." Bioinformatics 28, no. 15 (May 24, 2012): 2064–66. http://dx.doi.org/10.1093/bioinformatics/bts309.

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Stamatakis, Alexandros, Paul Hoover, and Jacques Rougemont. "A Rapid Bootstrap Algorithm for the RAxML Web Servers." Systematic Biology 57, no. 5 (October 1, 2008): 758–71. http://dx.doi.org/10.1080/10635150802429642.

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Zhang, Qi-Lin, Run-Qiu Feng, Min Li, Zhong-Long Guo, Li-Jun Zhang, Fang-Zhen Luo, Ya Cao, and Ming-Long Yuan. "The Complete Mitogenome of Pyrrhocoris tibialis (Hemiptera: Pyrrhocoridae) and Phylogenetic Implications." Genes 10, no. 10 (October 18, 2019): 820. http://dx.doi.org/10.3390/genes10100820.

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We determined the complete mitogenome of Pyrrhocoris tibialis (Hemiptera: Heteroptera: Pyrrhocoridae) to better understand the diversity and phylogeny within Pentatomomorpha, which is the second largest infra-order of Heteroptera. Gene content, gene arrangement, nucleotide composition, codon usage, ribosomal RNA (rRNA) structures, and sequences of the mitochondrial transcription termination factor were well conserved in Pyrrhocoroidea. Different protein-coding genes have been subject to different evolutionary rates correlated with the G + C content. The size of control regions (CRs) was highly variable among mitogenomes of three sequenced Pyrrhocoroidea species, with the P. tibialis CR being the largest. All the transfer RNA genes found in Pyrrhocoroidea had the typical clover leaf secondary structure, except for trnS1 (AGN), which lacked the dihydrouridine arm and possessed an unusual anticodon stem (9 bp vs. the normal 5 bp). A total of three different phylogenetic relationships among the five super-families of Pentatomomorpha were obtained using three analytical methods (MrBayes and RAxML under site-homogeneous models and PhyloBayes under a site-heterogeneous CAT + GTR model) and two mitogenomic datasets (nucleotides and amino acids). The tree topology test using seven methods statistically supported a phylogeny of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))) as the best topology, as recognized by both RAxML and MrBayes based on the two datasets.
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Liu, Kevin, C. Randal Linder, and Tandy Warnow. "RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation." PLoS ONE 6, no. 11 (November 21, 2011): e27731. http://dx.doi.org/10.1371/journal.pone.0027731.

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Stamatakis, A., F. Blagojevic, D. S. Nikolopoulos, and C. D. Antonopoulos. "Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell." Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology 48, no. 3 (August 9, 2007): 271–86. http://dx.doi.org/10.1007/s11265-007-0067-4.

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FRISCH, ANDREAS, MARTIN GRUBE, HIROYUKI KASHIWADANI, and YOSHIHITO OHMURA. "Arthoniaceae with reddish, K+ purple ascomata in Japan." Phytotaxa 356, no. 1 (June 13, 2018): 19. http://dx.doi.org/10.11646/phytotaxa.356.1.2.

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Arthonia sanguinaria is described as new to science. The East Asian Arthonia lopingensis and the widely distributed Arthonia picea are reported as new to Japan from Honshu and the Ogasawara Islands, respectively. The phylogenetic position of A. picea, A. sanguinaria and Coniocarpon cinnabarinum from the Ogasawara Islands is shown by RAxML and Bayesian analysis of mtSSU, nLSU and RPB2 sequence data. Our results confirm the polyphyletic origin of quinoid pigments in Arthoniaceae. A key is presented to the Arthoniaceae with reddish ascomata in Japan.
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Molloy, Erin K., and Tandy Warnow. "TreeMerge: a new method for improving the scalability of species tree estimation methods." Bioinformatics 35, no. 14 (July 2019): i417—i426. http://dx.doi.org/10.1093/bioinformatics/btz344.

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Abstract Motivation At RECOMB-CG 2018, we presented NJMerge and showed that it could be used within a divide-and-conquer framework to scale computationally intensive methods for species tree estimation to larger datasets. However, NJMerge has two significant limitations: it can fail to return a tree and, when used within the proposed divide-and-conquer framework, has O(n5) running time for datasets with n species. Results Here we present a new method called ‘TreeMerge’ that improves on NJMerge in two ways: it is guaranteed to return a tree and it has dramatically faster running time within the same divide-and-conquer framework—only O(n2) time. We use a simulation study to evaluate TreeMerge in the context of multi-locus species tree estimation with two leading methods, ASTRAL-III and RAxML. We find that the divide-and-conquer framework using TreeMerge has a minor impact on species tree accuracy, dramatically reduces running time, and enables both ASTRAL-III and RAxML to complete on datasets (that they would otherwise fail on), when given 64 GB of memory and 48 h maximum running time. Thus, TreeMerge is a step toward a larger vision of enabling researchers with limited computational resources to perform large-scale species tree estimation, which we call Phylogenomics for All. Availability and implementation TreeMerge is publicly available on Github (http://github.com/ekmolloy/treemerge). Supplementary information Supplementary data are available at Bioinformatics online.
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Dissertations / Theses on the topic "RaxML"

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Kool, Anneleen. "Desert Plants and Deserted Islands : Systematics and Ethnobotany in Caryophyllaceae." Doctoral thesis, Uppsala universitet, Systematisk biologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-179853.

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Background. Caryophyllaceae is a large and cosmopolitic flowering plant family, however the systematics of many of its basal groups has been unclear, due to a lack of unambiguous morphology. Some members of Caryophyllaceae are used medicinally, e.g. Corrigiola roots in Morocco. Monitoring the trade in medicinal plants is complicated due to the absence of useful identification characters in plant products such as roots, bark, and powders. This thesis aims at elucidating the systematics and the ethnobotany of some of the basal clades in Caryophyllaceae. Methods. A comprehensive sampling from herbarium as well as market and field collected material was used in systematic studies combining morphological investigation, molecular phylogenetic and molecular dating analyses. Results. The data show that Polycarpon is polyphyletic, that Sphaerocoma is sister to Pollichia and shows some intraspecific variation, that Sanctambrosia falls within the genus Spergularia, and that both Spergula and Spergularia are monophyletic. Preliminary data suggest that Polycarpaea is polyphyletic and should be split into three larger and several smaller genera, that the members of Paronychia subgen. Anaplonychia will need to be transferred to Herniaria to maintain monophyly, and that Caryophyllaceae emerged during the Paleocene. All the major extant lineages originated in the Oligocene and diversified later. Using molecular identification it was possible to identify around 50% of the Moroccan medicinal roots to species level and an additional 30% to genus level. Discussion and conclusions. The polyphyletic Polycarpon needs to be split into at least three separate genera, but no name changes were made pending further research. The two species of Sphaerocoma were merged into one species with two subspecies. The San Ambrosio Island endemic Sanctambrosia, the only tree-like plant in Caryophyllaceae, is probably the result of a long distance dispersal event and its woody habit and gynodioecy are probably caused by inbreeding depression. Sanctambrosia manicata is transferred to Spergularia. Molecular identification put into practice on traded medicinal roots has a somewhat lower success rate than most theoretical studies, indicating that a global barcoding database would need to include reference sequences from a broad range of populations for each species.
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Raml, Thomas Oliver [Verfasser], Hans-Jürgen [Akademischer Betreuer] Roder, and Jörg H. [Akademischer Betreuer] Kleeff. "Operative Therapie der Sigmadivertikulitis an einem Krankenhaus der Schwerpunktversorgung / Thomas Oliver Raml. Gutachter: Hans-Jürgen Roder ; Jörg H. Kleeff. Betreuer: Hans-Jürgen Roder." München : Universitätsbibliothek der TU München, 2014. http://d-nb.info/1047185350/34.

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Wideberg, Robert. "RESTful Services in an Enterprise Environment : A Comparative Case Study of Specification Formats and HATEOAS." Thesis, KTH, Skolan för datavetenskap och kommunikation (CSC), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-172833.

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RESTful services are becoming increasingly popular. This work, that was carried out at Scania IT, investigates how a RESTful service should be designed and specified so that it meets the demands of an enterprise environment. In particular, this report will focus on documentation and validation of RESTful services, i.e. specifications. These are important aspects in an enterprise environment. The investigation consists of a comparative case study of four specification formats and Hypermedia As The Engine Of Application State (HATEOAS). The results show that the most commonly used specification formats have flaws. They also suggest that Swagger and RAML (RESTful API Modeling Language) are the two most mature formats. The results also show that HATEOAS, which is a more dynamic approach, can be useful in an enterprise environment but that it requires careful design.
REST-tjänster blir alltmer populära. Detta arbete, som utfördes på Scania IT, undersöker hur en REST-tjänst bör designas och specifieras för att möta de krav som finns i en enterprise-miljö. Specifikt kommer denna rapport att fokusera på dokumentation och validering av REST-tjänster, med andra ord specifikationer. Dessa är viktiga aspekter i en enterprise-miljö. Undersökningen består av en jämförande fallstudie med fyra specifikationsformat samt Hypermedia As The Engine Of Application State (HATEOAS). Resultaten visar att de mest vanligt förekommande specifikationsformaten har brister. De antyder också att Swagger och RAML (RESTful API Modeling Language) är de två mest mogna formaten. Resultaten visar också att HATEOAS, som är ett mer dynamiskt angreppssätt, kan vara användbart i en enterprise-miljö men att det kräver omsorgsfull design.
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Lee, Eun Jung 1974. "Phylogeographic Patterns of Tylos (Isopoda: Oniscidea) in the Pacific Region Between Southern California and Central Mexico, and Mitochondrial Phylogeny of the Genus." Thesis, 2012. http://hdl.handle.net/1969.1/148085.

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Isopods in the genus Tylos are distributed in tropical and subtropical sandy intertidal beaches throughout the world. These isopods have biological characteristics that are expected to severely restrict their long-distance dispersal potential: (1) they are direct developers (i.e., as all peracarids, they lack a planktonic stage); (2) they cannot survive in the sea for long periods of immersion (i.e., only a few hours); (3) they actively avoid entering the water; and (4) they are restricted to the sandy intertidal portion that is wet, but not covered by water. Because of these traits, high levels of genetic differentiation are anticipated among allopatric populations of Tylos. We studied the phylogeographic patterns of Tylos in the northern East Pacific region between southern California and central Mexico, including the Gulf of California. We discovered high levels of cryptic biodiversity for this isopod, consistent with expectations from its biology. We interpreted the phylogeographic patterns of Tylos in relation to past geological events in the region, and compared them with those of Ligia, a co-distributed non-vagile coastal isopod. Furthermore, we assessed the usefulness of the shape of the ventral plates of the fifth pleonite for distinguishing genetically divergent lineages of Tylos in the study area. Finally, mitochondrial phylogenenetic analyses to identify the most appropriate outgroup taxa for Tylos in the study area, which included 17 of the 21 currently recognized species, provided important insights on the evolutionary history of this genus.
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Books on the topic "RaxML"

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Ḥāyy, Nājī. Ḥabbat raml. al-Shāriqah: Dāʼirat al-Thaqāfah wa-al-Iʻlām, 1993.

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Ḥayy, Nājī. Ḥabbat raml. al-Shāriqah: Dāʾirat al-Thaqāfah wa-al-Iʻlām, 1993.

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Dhākirat al-raml. al-Rabāṭ: Dār al-Amān, 2008.

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ʻAmrī, Muḥammad ʻAbd al-Salām. Ṣamt al-raml. al-Qāhirah: Dār al-Hilāl, 2002.

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Kahlil, Gibran. Raml wa-zabad. 2nd ed. al-Qāhirah: Dār al-ʻArab, 1986.

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Takerly, Fouad A. Khatam a raml. Beirut: Da Al Adab, 1995.

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ʻArāʼis al-raml: Riwāyah. al-Jazāʼir: Dār al-Tanwīr, 2013.

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Allāh, Āṣif ʻAbd. Waqt min raml: Shiʻr. Dimashq: Ittiḥād al-Kuttāb al-ʻArab, 1992.

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al-Dīn, Wahīb Sarāy. Nafād al-raml: Qiṣaṣ. Dimashq: Ittiḥād al-Kuttāb al-ʻArab, 1998.

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Mayhūb, Muḥammad Āyat. Ḥurūf al-raml: Riwāyah. [Tunisia]: M.Ā. Mayhūb, 1994.

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Book chapters on the topic "RaxML"

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Ott, Michael, and Alexandros Stamatakis. "Preparing RAxML for the SPEC MPI Benchmark Suite." In High Performance Computing in Science and Engineering, Garching/Munich 2009, 757–68. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-13872-0_63.

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Stamatakis, Alexandros, Michael Ott, and Thomas Ludwig. "RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs." In Lecture Notes in Computer Science, 288–302. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11535294_25.

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Ashikhmin, Nikita, Gleb Radchenko, and Andrei Tchernykh. "RAML-Based Mock Service Generator for Microservice Applications Testing." In Communications in Computer and Information Science, 456–67. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-71255-0_37.

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Conference papers on the topic "RaxML"

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Coelho, Micaella, Carla Osthoff, and Kary Ocaña. "Avaliação do RAxML no Supercomputador Santos Dumont." In XI Simpósio Brasileiro de Bioinformática. Sociedade Brasileira de Computação - SBC, 2019. http://dx.doi.org/10.5753/bsb_estendido.2018.8802.

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Análises filogenéticas apoiam estudos sobre a vida evolutiva dos organismos. Ferramentas otimizadas como RAxML, baseadas em algoritmos de máxima verossimilhança, geram alto custo computacional pelos inúmeros cálculos para processar grande quantidades de dados. O uso eficiente dessas ferramentas em ambientes paralelos é requerido. O presente trabalho visa explorar o desempenho do RAxML em supercomputadores explorando características de configuração do ambiente, programa e dados
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Pfeiffer, Wayne, and Alexandros Stamatakis. "Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code." In Distributed Processing, Workshops and Phd Forum (IPDPSW 2010). IEEE, 2010. http://dx.doi.org/10.1109/ipdpsw.2010.5470900.

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Malakonakis, Pavlos, Andreas Brokalakis, Nikolaos Alachiotis, Evripides Sotiriades, and Apostolos Dollas. "Exploring Modern FPGA Platforms for Faster Phylogeny Reconstruction with RAxML." In 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2020. http://dx.doi.org/10.1109/bibe50027.2020.00024.

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Blagojevic, Filip, Alexandros Stamatakis, Christos D. Antonopoulos, and Dimitrios S. Nikolopoulos. "RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine." In 2007 IEEE International Parallel and Distributed Processing Symposium. IEEE, 2007. http://dx.doi.org/10.1109/ipdps.2007.370267.

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Zhu, Pengfei, Ren Qi, Qinghua Hu, Qilong Wang, Changqing Zhang, and Liu Yang. "Beyond Similar and Dissimilar Relations : A Kernel Regression Formulation for Metric Learning." In Twenty-Seventh International Joint Conference on Artificial Intelligence {IJCAI-18}. California: International Joint Conferences on Artificial Intelligence Organization, 2018. http://dx.doi.org/10.24963/ijcai.2018/450.

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Most existing metric learning methods focus on learning a similarity or distance measure relying on similar and dissimilar relations between sample pairs. However, pairs of samples cannot be simply identified as similar or dissimilar in many real-world applications, e.g., multi-label learning, label distribution learning or tasks with continuous decision values. To this end, in this paper we propose a novel relation alignment metric learning (RAML) formulation to handle the metric learning problem in those scenarios. Since the relation of two samples can be measured by the difference degree of the decision values, motivated by the consistency of the sample relations in the feature space and decision space, our proposed RAML utilizes the sample relations in the decision space to guide the metric learning in the feature space. Specifically, our RAML method formulates metric learning as a kernel regression problem, which can be efficiently optimized by the standard regression solvers. We carry out several experiments on the single-label classification, multi-label classification, and label distribution learning tasks, to demonstrate that our method achieves favorable performance against the state-of-the-art methods.
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L. Sosa-Ríos, Manuel, Jonas R. Pesente, Luís F. C. Alberto, and Rodrigo A. Ramos. "Estudo de um Ciclo Limite Resultante da Interação entre Estabilizadores de Sistemas de Potência e Controladores de Elos HVDC." In Simpósio Brasileiro de Sistemas Elétricos - SBSE2020. sbabra, 2020. http://dx.doi.org/10.48011/sbse.v1i1.2196.

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Este artigo apresenta um estudo de interações entre controladores de elos de corrente contínua (HVDC) e estabilizadores de sistemas de potência (PSS) que levam ao aparecimento de ciclos limites estáveis. O sistema estudado é composto por um grupo de unidades geradoras interligado a um barramento infinito através de um elo HVDC, estrutura similar a uma versão simplificada do sistema de transmissão entre o setor de 50 Hz de Itaipu e o sistema interligado nacional do Brasil. Os principais controladores envolvidos no ciclo limite são o limitador de Ângulo Mínimo de Disparo do Retificador (RAML) do HVDC e o PSS do grupo de geradores. Também é mostrado que o ciclo limite coexiste com uma condição de equilíbrio estável e que o sistema atinge uma condição de oscilação sustentada após uma grande perturbação. Esta condição de oscilação é indesejada e o trabalho mostra que um ajuste coordenado dos parâmetros do RAML e do estabilizador de frequência (STAB) evitam o surgimento do ciclo limite, ainda em caso de grandes perturbações.
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Jiao, Weiwei, Wenbin Yu, Long Cheng, Canfeng Chen, and Jian Ma. "RAML: Range-Boundary Aware Mobility-Assisted Localization Scheme for Wireless Sensor Networks." In 2009 International Conference on Scalable Computing and Communications; Eighth International Conference on Embedded Computing. IEEE, 2009. http://dx.doi.org/10.1109/embeddedcom-scalcom.2009.22.

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Surace, Domenica, Patrizia Broccia, Youssef Salemi, and Massimo Iovane. "Installation of a Produced-Water Treatment System on Raml Field (Western Desert), Egypt." In SPE Annual Technical Conference and Exhibition. Society of Petroleum Engineers, 2010. http://dx.doi.org/10.2118/135725-ms.

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