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16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers...

Materias / palabras clave: Phylogenetic tree; Biology; Coronavirus; Virology; Sanger sequencing; Genome; Phylogenetics; Virus; Betacoronavirus; DNA sequencing; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Sequence analysis

We have designed two taxon-selective primers for the internal transcribed spacer (ITS) region in the nuclear ribosomal repeat unit. These primers, ITS1-F and ITS4-B, were intended to be specific to fungi and basidiomycet...

The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a...

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. He...

The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comp...

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been...

Materias / palabras clave: Phylogenetic tree; Selection (genetic algorithm); Computational biology; Evolutionary biology; Model selection; Biology; Phylogenetics; Computer science; Genetics; Artificial intelligence; Gene

PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main...

Materias / palabras clave: Biology; Ribosomal DNA; Spacer DNA; Heterochromatin; Internal transcribed spacer; Genetics; Phylogenetic tree; Ribosomal RNA; Intergenic region; Ploidy; Phylogenetics; Chromosome

Comparative studies of the relationship between two phenotypes, or between a phenotype and an environment, are frequently carried out by invalid statistical methods. Most regression, correlation, and contingency table me...

Materias / palabras clave: Metagenomics; Biology; Phylogenetic tree; 16S ribosomal RNA; Gene; Computational biology; Phylogenetics; Microbiome; Genetics; Ribosomal RNA; Genome; Evolutionary biology

The many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. However, k...

The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not b...

Phylogenies are extremely useful tools, not only for establishing genealogical relationships among a group of organisms or their parts (e.g. genes), but also for a variety of research once the phylogenies are estimated. ...

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= nei...

We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tr...

Las relaciones filogenéticas entre las especies del género Pseudopaludicola son analizadas en base a caracteres externos y osteológicos. Se estudiaron once especies de Physalaemus las que fueron empleadas como grupo e...

BACKGROUND: The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, a...

BACKGROUND: the analysis of microbial communities through dna sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, vis...

Materias / palabras clave: biology, fundamental biology, translational biology, biomedical biology, evolutionary biology, phylogenetics; Science: Biology (General)

Materias / palabras clave: ecology, biodiversity, evolutionary biology, phylogenetics, palaeontology, developmental biology; Science: Biology (General): Ecology; Science: Biology (General): Evolution

Materias / palabras clave: evolutionary biology, phylogenetics, palaeontology; Science: Biology (General): Evolution

Materias / palabras clave: genome analysis, sequence analysis, phylogenetics, gene expression, systems biology; Science: Biology (General)