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Phylogenomic
Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields of phylogenetics and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Four major areas fall under phylogenomics: * Prediction of gene function * Establishment and clarification of evolutionary relationships * Gene family evolution * Prediction and retracing lateral gene transfer. The ultimate goal of phylogenomics is to reconstruct the evolutionary history of species through their genomes. This history is usually inferred from a series of genomes by using a genome evolution model and standard statistical inference methods (e.g. Bayesian inference or ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to resolving paraphyletic groups, this method also reassigns taxonomic ranks algorithmically, updating names in both cases. Information for archaea was added in 2020, along with a species classification based on average nucleotide identity. Each update incorporates new genomes as well as automated and manual curation of the taxonomy. An open-source tool called GTDB-Tk is available to classify draft genomes into the GTDB hierarchy. The GTDB system, via GTDB-Tk, has been used to catalogue not-yet-named bacteria in the human gut microbiome and other metagenomic sources. The GTDB is incorporated into the '' Bergey's Manual of Systematics of Archaea and Bacteria'' in 2019 as its phylogenomic resource. Methodology The genomes used to construct the phyloge ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Plants+HC+SAR Megagroup
Diaphoretickes is a major group of eukaryotic organisms spanning over 400,000 species. The majority of the earth's biomass that carries out photosynthesis belongs to Diaphoretickes. In older classification systems, members of the Diaphoretickes were variously placed in the kingdoms Protozoa or Protista. Etymology The name Diaphoretickes derives (''diaforetikés'') meaning diverse, dissimilar, referring to the wide morphological and cellular diversity among members of this clade. History Eukaryotes, organisms whose cells contain a nucleus, have been traditionally grouped into four kingdoms: animals, plants, fungi and protists. In the late 20th century, molecular phylogenetic analyses revealed that protists are a paraphyletic assortment of many independent evolutionary lineages or clades, from which animals, fungi and plants evolved. However, the relationships between these clades remained difficult to assess due to technological limitations. Starting in the early 2000s, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Archaeopteryx (evolutionary Tree Visualization And Analysis)
Archaeopteryx is an interactive computer software program, written in Java, for viewing, editing, and analyzing phylogenetic trees. This type of program can be used for a variety of analyses of molecular data sets, but is particularly designed for phylogenomics Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields .... Besides tree description formats with limited expressiveness (such as Newick/New Hamphshire, Nexus), it also implements the phyloXML format. Archaeopteryx is the successor to Java program ''A Tree Viewer'' (ATV). References External linksphyloXML * ttp://www.phylosoft.org/archaeopteryx/ Archaeopteryx {{genomics-footer Phylogenetics software ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Jonathan Eisen
Jonathan Andrew Eisen (born August 31, 1968) is an American evolutionary biologist, currently working at University of California, Davis. His academic research is in the fields of evolutionary biology, genomics and microbiology and he is the academic editor-in-chief of the open access journal '' PLOS Biology''. Education Eisen completed his undergraduate studies at Harvard College in 1990, earning an AB degree in biology. He graduated as a Doctor of Philosophy from Stanford University in 1998 with a thesis on the evolution of DNA repair genes, proteins, and processes in 1998, supervised by Philip Hanawalt. Research Eisen's research focuses on the origin of novelty, how new processes and functions originate in living things. To study this, he focuses on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis. Eisen, together with Nick Barton, Derek E.G. Briggs, David B. Goldstein, and Nipam H. Patel, authored the undergraduate t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Computational Phylogenetics
Computational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, Heuristic (computer science), heuristics, and approaches involved in Phylogenetics, phylogenetic analyses. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes, species, or taxa. Maximum likelihood estimation, Maximum likelihood, Maximum parsimony (phylogenetics), parsimony, Bayesian inference in phylogeny, Bayesian, and minimum evolution are typical optimality criteria used to assess how well a phylogenetic tree topology describes the sequence data. Nearest Neighbour Interchange (NNI), Subtree Prune and Regraft (SPR), and Tree Bisection and Reconnection (TBR), known as tree rearrangements, are deterministic algorithms to search for optimal or the best phylogenetic tree. The space and the landscape of searching for the optimal phylogenetic tree is known as phylogeny search space. Maximum Likelihood (al ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Plants
Plants are the eukaryotes that form the kingdom Plantae; they are predominantly photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with cyanobacteria to produce sugars from carbon dioxide and water, using the green pigment chlorophyll. Exceptions are parasitic plants that have lost the genes for chlorophyll and photosynthesis, and obtain their energy from other plants or fungi. Most plants are multicellular, except for some green algae. Historically, as in Aristotle's biology, the plant kingdom encompassed all living things that were not animals, and included algae and fungi. Definitions have narrowed since then; current definitions exclude fungi and some of the algae. By the definition used in this article, plants form the clade Viridiplantae (green plants), which consists of the green algae and the embryophytes or land plants ( hornworts, liverworts, mosses, lycophytes, ferns, conifers and other ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Supertree
A supertree is a single phylogenetic tree assembled from a combination of smaller phylogenetic trees, which may have been assembled using different datasets (e.g. morphological and molecular) or a different selection of taxa. Supertree algorithms can highlight areas where additional data would most usefully resolve any ambiguities. The input trees of a supertree should behave as samples from the larger tree. Construction methods The construction of a supertree scales exponentially with the number of taxa included; therefore for a tree of any reasonable size, it is not possible to examine every possible supertree and weigh its success at combining the input information. Heuristic methods are thus essential, although these methods may be unreliable; the result extracted is often biased or affected by irrelevant characteristics of the input data. The most well known method for supertree construction is Matrix Representation with Parsimony (MRP), in which the input source trees ar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Microbial Phylogenetics
Microbial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution. To study these relationships biologists rely on comparative genomics, as physiology and comparative anatomy are not possible methods. History 1960s–1970s Microbial phylogenetics emerged as a field of study in the 1960s, scientists started to create genealogical trees based on differences in the order of amino acids of proteins and nucleotides of genes instead of using comparative anatomy and physiology. One of the most important figures in the early stage of this field is Carl Woese, who in his researches, focused on Bacteria, looking at RNA instead of proteins. More specifically, he decided to compare the small subunit ribosomal RNA (16rRNA) oligonucleotides. Matching oligonucleotides in different bacteria could be compared to one another to determine how closely the organisms were related. In 1977, after collecting and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
PhylomeDB
PhylomeDB is a public biological database for complete catalogs of gene phylogenies ( phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming and evolutionary model testing. PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well as a web API that facilitates cross linking trees from external sources. Finally, phylomeDB provides an advanced tree visualization interface based on the ETE toolkit,{{cite journal , last=Huerta-Cepas, J, author2= Dopazo, J, author3=Gabaldón, T , date=Jan ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Cryptomonads
The cryptomonads (or cryptophytes) are a superclass of algae, most of which have plastids. They are traditionally considered a division of algae among phycologists, under the name of Cryptophyta. They are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10–50 μm in size and flattened in shape, with an anterior groove or pocket. At the edge of the pocket there are typically two slightly unequal flagella. Some may exhibit mixotrophy. They are classified as superclass Cryptomonada, which is divided into two classes: heterotrophic Goniomonadea and phototrophic Cryptophyceae. The two groups are united under three shared morphological characteristics: presence of a periplast, ejectisomes with secondary scroll, and mitochondrial cristae with flat tubules. Genetic studies as early as 1994 also supported the hypothesis that ''Goniomonas'' was sister to Cryptophyceae. A study in 2018 found strong evidence that the common ancestor of Cryp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Sequence Alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix (mathematics), matrix. Gaps are inserted between the Residue (chemistry), residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences such as calculating the Edit distance, distance cost between strings in a natural language, or to display financial data. Interpretation If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence ali ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
Phylogenetics
In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical data and observed heritable traits of DNA sequences, protein amino acid sequences, and morphology. The results are a phylogenetic tree—a diagram depicting the hypothetical relationships among the organisms, reflecting their inferred evolutionary history. The tips of a phylogenetic tree represent the observed entities, which can be living taxa or fossils. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the taxa represented on the tree. An unrooted tree diagram (a network) makes no assumption about directionality of character state transformation, and does not show the origin or "root" of the taxa in question. In addition to their use for inferring phylogenetic pa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
