Search Results - "Molecular biology and evolution"

MEGA11: Molecular Evolutionary Genetics Analysis Version 11 by Tamura, Koichiro, Stecher, Glen, Kumar, Sudhir

“…Abstract The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular…”
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eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale by Cantalapiedra, Carlos P, Hernández-Plaza, Ana, Letunic, Ivica, Bork, Peer, Huerta-Cepas, Jaime

“…Abstract Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging…”
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BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes by Manni, Mosè, Berkeley, Matthew R, Seppey, Mathieu, Simão, Felipe A, Zdobnov, Evgeny M

“…Abstract Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the…”
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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era by Minh, Bui Quang, Schmidt, Heiko A, Chernomor, Olga, Schrempf, Dominik, Woodhams, Michael D, von Haeseler, Arndt, Lanfear, Robert

“…Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using…”
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Molecular Evolutionary Genetics Analysis (MEGA) for macOS by Stecher, Glen, Tamura, Koichiro, Kumar, Sudhir

“…Abstract The Molecular Evolutionary Genetics Analysis (MEGA) software enables comparative analysis of molecular sequences in phylogenetics and evolutionary…”
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TimeTree 5: An Expanded Resource for Species Divergence Times by Kumar, Sudhir, Suleski, Michael, Craig, Jack M, Kasprowicz, Adrienne E, Sanderford, Maxwell, Li, Michael, Stecher, Glen, Hedges, S Blair

“…Abstract We present the fifth edition of the TimeTree of Life resource (TToL5), a product of the timetree of life project that aims to synthesize published…”
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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms by Kumar, Sudhir, Stecher, Glen, Li, Michael, Knyaz, Christina, Tamura, Koichiro

“…The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report…”
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ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models by Darriba, Diego, Posada, David, Kozlov, Alexey M, Stamatakis, Alexandros, Morel, Benoit, Flouri, Tomas

“…Abstract ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid…”
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UFBoot2: Improving the Ultrafast Bootstrap Approximation by Hoang, Diep Thi, Chernomor, Olga, von Haeseler, Arndt, Minh, Bui Quang, Vinh, Le Sy

“…The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the…”
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MBE Citation Classics (2018 Edition) by Kumar, Sudhir, Rowe, Heather

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DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets by Rozas, Julio, Ferrer-Mata, Albert, Sánchez-DelBarrio, Juan Carlos, Guirao-Rico, Sara, Librado, Pablo, Ramos-Onsins, Sebastián E, Sánchez-Gracia, Alejandro

“…We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version of the popular tool for performing exhaustive population genetic analyses…”
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BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics by Waterhouse, Robert M, Seppey, Mathieu, Simão, Felipe A, Manni, Mosè, Ioannidis, Panagiotis, Klioutchnikov, Guennadi, Kriventseva, Evgenia V, Zdobnov, Evgeny M

“…Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of…”
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PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses by Lanfear, Robert, Frandsen, Paul B, Wright, April M, Senfeld, Tereza, Calcott, Brett

“…PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2…”
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Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper by Huerta-Cepas, Jaime, Forslund, Kristoffer, Coelho, Luis Pedro, Szklarczyk, Damian, Jensen, Lars Juhl, von Mering, Christian, Bork, Peer

“…Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most…”
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TimeTree: A Resource for Timelines, Timetrees, and Divergence Times by Kumar, Sudhir, Stecher, Glen, Suleski, Michael, Hedges, S Blair

“…Evolutionary information on species divergence times is fundamental to studies of biodiversity, development, and disease. Molecular dating has enhanced our…”
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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets by Kumar, Sudhir, Stecher, Glen, Tamura, Koichiro

“…We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for…”
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RASP 4: Ancestral State Reconstruction Tool for Multiple Genes and Characters by Yu, Yan, Blair, Christopher, He, Xingjin

“…Abstract With the continual progress of sequencing techniques, genome-scale data are increasingly used in phylogenetic studies. With more data from throughout…”
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SMS: Smart Model Selection in PhyML by Lefort, Vincent, Longueville, Jean-Emmanuel, Gascuel, Olivier

“…Model selection using likelihood-based criteria (e.g., AIC) is one of the first steps in phylogenetic analysis. One must select both a substitution matrix and…”
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SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model by Haller, Benjamin C, Messer, Philipp W

“…Abstract With the desire to model population genetic processes under increasingly realistic scenarios, forward genetic simulations have become a critical part…”
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New Methods to Calculate Concordance Factors for Phylogenomic Datasets by Minh, Bui Quang, Hahn, Matthew W, Lanfear, Robert

“…Abstract We implement two measures for quantifying genealogical concordance in phylogenomic data sets: the gene concordance factor (gCF) and the novel site…”
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