|
T-REX (webserver)
T-REX (Tree and Reticulogram Reconstruction) is a freely available web server, developed at the department of Computer Science of the Université du Québec à Montréal, dedicated to the inference, validation and visualization of phylogenetic trees and phylogenetic networks. The T-REX web server allows the users to perform several popular methods of phylogenetic analysis as well as some new phylogenetic applications for inferring, drawing and validating phylogenetic trees and networks. Phylogenetic inference The following methods for inferring and validating phylogenetic trees using distances are available: Neighbor joining (NJ),NINJA large-scale Neighbor Joining''k'') = exp(-''k'')), and the constant a is a tuning factor accounting for the deviation intensity (as described in Guindon and Gascuel (2002), the value of a was set to 0.8). The random trees generated by this procedure have depth of O(log (''n'')). References {{Reflist die External links Official T-REX Web server p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Web Server
A web server is computer software and underlying hardware that accepts requests via HTTP (the network protocol created to distribute web content) or its secure variant HTTPS. A user agent, commonly a web browser or web crawler, initiates communication by making a request for a web page or other resource using HTTP, and the server responds with the content of that resource or an error message. A web server can also accept and store resources sent from the user agent if configured to do so. The hardware used to run a web server can vary according to the volume of requests that it needs to handle. At the low end of the range are embedded systems, such as a router that runs a small web server as its configuration interface. A high-traffic Internet website might handle requests with hundreds of servers that run on racks of high-speed computers. A resource sent from a web server can be a preexisting file (static content) available to the web server, or it can be generated ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MUSCLE (alignment Software)
MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain. The method was published by Robert C. Edgar in two papers in 2004. The first paper, published in ''Nucleic Acids Research'', introduced the sequence alignment algorithm. The second paper, published in ''BMC Bioinformatics'', presented more technical details. Algorithm The MUSCLE algorithm proceeds in three stages: the ''draft progressive'', ''improved progressive'', and ''refinement'' stage. Stage 1: Draft Progressive In this first stage, the algorithm produces a multiple alignment, emphasizing speed over accuracy. This step begins by computing the k-mer distance for every pair of input sequences to create a distance matrix. UPGMA clusters the distance matrix to produce a binary tree. From this tree a progressive alignment is constructed, beginning with the creation of profiles for each leaf of the tree ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Data Visualization Software
In the pursuit of knowledge, data (; ) is a collection of discrete values that convey information, describing quantity, quality, fact, statistics, other basic units of meaning, or simply sequences of symbols that may be further interpreted. A datum is an individual value in a collection of data. Data is usually organized into structures such as tables that provide additional context and meaning, and which may themselves be used as data in larger structures. Data may be used as variables in a computational process. Data may represent abstract ideas or concrete measurements. Data is commonly used in scientific research, economics, and in virtually every other form of human organizational activity. Examples of data sets include price indices (such as consumer price index), unemployment rates, literacy rates, and census data. In this context, data represents the raw facts and figures which can be used in such a manner in order to capture the useful information out of it. Dat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Distance Matrix
In mathematics, computer science and especially graph theory, a distance matrix is a square matrix (two-dimensional array) containing the distances, taken pairwise, between the elements of a set. Depending upon the application involved, the ''distance'' being used to define this matrix may or may not be a metric. If there are elements, this matrix will have size . In graph-theoretic applications the elements are more often referred to as points, nodes or vertices. Non-metric distance matrix In general, a distance matrix is a weighted adjacency matrix of some graph. In a network, a directed graph with weights assigned to the arcs, the distance between two nodes of the network can be defined as the minimum of the sums of the weights on the shortest paths joining the two nodes. This distance function, while well defined, is not a metric. There need be no restrictions on the weights other than the need to be able to combine and compare them, so negative weights are used in some appli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Newick
Newick is a village, civil parish and electoral ward in the Lewes District of East Sussex, England. It is located on the A272 road east of Haywards Heath. The parish church, St. Mary's, dates mainly from the Victorian era, but still has a Norman window. Zion Chapel, a Strict Baptist chapel, was built in 1834 and converted to flats in 2001. Newick Evangelical Free Church, originally a mission hall, opened in 1892. The village is home to three pubs (''The Crown Inn'', ''The Royal Oak'', and ''The Bull Inn''), one restaurant (Newick Tandoori), a butcher, a baker, a pharmacy, as well as a number of other businesses. There is also a primary school, a health centre, a village hall known originally as the 'Derek Hall', and a post office. Like many other places in Sussex, Newick holds an annual Bonfire Night celebration on the Saturday before Lewes Bonfire Night. Many of the local bonfire societies join the procession. History Newick was a dispersed settlement until the Second Wo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Robinson–Foulds Metric
The Robinson–Foulds or symmetric difference metric, often abbreviated as the RF distance, is a simple way to calculate the distance between phylogenetic trees. It is defined as ( + ) where is the number of partitions of data implied by the first tree but not the second tree and is the number of partitions of data implied by the second tree but not the first tree (although some software implementations divide the RF metric by 2 and others scale the RF distance to have a maximum value of 1). The partitions are calculated for each tree by removing each branch. Thus, the number of eligible partitions for each tree is equal to the number of branches in that tree. RF distances have been criticized as biased, but they represent a relatively intuitive measure of the distances between phylogenetic trees and therefore remain widely used (the original 1981 paper describing Robinson-Foulds distances was cited more than 200 times in 2019 based on Google Scholar). Nevertheless, the biases inhe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Sequence Alignment
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ClustalW
Clustal is a series of widely used computer programs used in bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below. The analysis of each tool and its algorithm are also detailed in their respective categories. Available operating systems listed in the sidebar are a combination of the software availability and may not be supported for every current version of the Clustal tools. Clustal Omega has the widest variety of operating systems out of all the Clustal tools. History There have been many variations of the Clustal software, all of which are listed below: * Clustal: The original software for multiple sequence alignments, created by Des Higgins in 1988, was based on deriving phylogenetic trees from pairwise sequences of amino acids or nucleotides. * ClustalV: The second generation of the Clustal software was released in 1992 and was a rewrite of the original Clustal package. It int ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MAFFT
In bioinformatics, MAFFT (for multiple alignment using fast Fourier transform) is a program used to create multiple sequence alignments of amino acid or nucleotide sequences. Published in 2002, the first version of MAFFT used an algorithm based on progressive alignment, in which the sequences were clustered with the help of the Fast Fourier Transform. Subsequent versions of MAFFT have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and the addition of new sequences to existing alignments. See also * Sequence alignment software * Clustal Clustal is a series of widely used computer programs used in bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below. The analysis of each tool and its a ... References External links * MAFFT Online ServerMAFFT ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Université Du Québec à Montréal
The Université du Québec à Montréal (English: University of Quebec in Montreal), also known as UQAM, is a French-language public university based in Montreal, Quebec, Canada. It is the largest constituent element of the Université du Québec system. UQAM was founded on April 9, 1969, by the government of Quebec, through the merger of the École des beaux-arts de Montréal, a fine arts school; the Collège Sainte-Marie, a classical college; and a number of smaller schools. Although part of the UQ network, UQAM possesses a relative independence which allows it to print its own diplomas and choose its rector. In the fall of 2018, the university welcomed some 40,738 students, including 3,859 international students from 95 countries, in a total of 310 distinct programs of study, managed by six faculties (Arts, Education, Communication, Political Science and Law, Science and Social science) and one school (Management). It offers Bachelors, Masters, and Doctoral degrees. It is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Horizontal Gene Transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms. HGT is influencing scientific understanding of higher order evolution while more significantly shifting perspectives on bacterial evolution. Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria, and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created Bactericide, pesticides and in the evolution, maintenance, and transmission of virulence. It often involves Temperateness (virology), temperate bacteriophages and plasmids. Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTA Format
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics. The simplicity of FASTA format makes it easy to manipulate and parse sequences using text-processing tools and scripting languages like the R programming language, Python, Ruby, Haskell, and Perl. Original format & overview The original FASTA/Pearson format is described in the documentation for the FASTA suite of programs. It can be downloaded with any free distribution of FASTA (see fasta20.doc, fastaVN.doc or fastaVN.me—where VN is the Version Number). In the original format, a sequence was represented as a series of lines, each of whic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
.svg "Click for more on -> Horizontal Gene Transfer"){kind=spacer}