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BAli-Phy
BAli-Phy is a free software program for simultaneously estimating a multiple sequence alignment and its phylogenetic tree. BAli-Phy achieves high accuracy in alignment estimation by using information from the co-estimated phylogeny. BAli-Phy takes alignment uncertainty into account while estimating the phylogeny by averaging over possible alignments. Unlike most phylogeny inference software, input sequences need not be aligned beforehand. This differs from traditional approaches to alignment and phylogeny estimation, which first estimate the alignment without a high-quality tree estimate, and then estimate the tree given the alignment. BAli-Phy produces a Bayesian posterior distribution on both the alignments and the tree. The software shows uncertainty in both the alignment and the tree. BAli-Phy uses Markov chain Monte Carlo methods for estimation. It can take several days to run. Alignment uncertainty Alignment uncertainty stems from two main sources: near-optimal ali ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Alignment Software
This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins. Database search only *Sequence type: protein or nucleotide Pairwise alignment *Sequence type: protein or nucleotide **Alignment type: local or global Multiple sequence alignment *Sequence type: protein or nucleotide. **Alignment type: local or global Genomics analysis *Sequence type: protein or nucleotide Motif finding *Sequence type: protein or nucleotide Benchmarking Alignment viewers, editors Please see List of alignment visualization software. Short-read sequence alignment See also * List of open source bioinformatics software References {{Reflist Seq Sequence In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Sequence Alignment
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences. Alignments highlight mutation events such as point mutations (single amino acid or nucleotide changes), insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides. Multiple sequence alignments require more sophisticated methodologies than pairwise alignments, as they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibiti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Windows
Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sectors of the computing industry – Windows (unqualified) for a consumer or corporate workstation, Windows Server for a Server (computing), server and Windows IoT for an embedded system. Windows is sold as either a consumer retail product or licensed to Original equipment manufacturer, third-party hardware manufacturers who sell products Software bundles, bundled with Windows. The first version of Windows, Windows 1.0, was released on November 20, 1985, as a graphical operating system shell for MS-DOS in response to the growing interest in graphical user interfaces (GUIs). The name "Windows" is a reference to the windowing system in GUIs. The 1990 release of Windows 3.0 catapulted its market success and led to various other product families ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MacOS
macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. Within the market of Desktop computer, desktop and laptop computers, it is the Usage share of operating systems#Desktop and laptop computers, second most widely used desktop OS, after Microsoft Windows and ahead of all Linux distributions, including ChromeOS and SteamOS. , the most recent release of macOS is MacOS Sequoia, macOS 15 Sequoia, the 21st major version of macOS. Mac OS X succeeded classic Mac OS, the primary Mac operating systems, Macintosh operating system from 1984 to 2001. Its underlying architecture came from NeXT's NeXTSTEP, as a result of NeXT#1997–2006: Acquisition by Apple, Apple's acquisition of NeXT, which also brought Steve Jobs back to Apple. The first desktop version, Mac OS X 10.0, was released on March 24, 2001. Mac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UNIX
Unix (, ; trademarked as UNIX) is a family of multitasking, multi-user computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, and others. Initially intended for use inside the Bell System, AT&T licensed Unix to outside parties in the late 1970s, leading to a variety of both academic and commercial Unix variants from vendors including University of California, Berkeley ( BSD), Microsoft (Xenix), Sun Microsystems ( SunOS/ Solaris), HP/ HPE ( HP-UX), and IBM ( AIX). The early versions of Unix—which are retrospectively referred to as " Research Unix"—ran on computers such as the PDP-11 and VAX; Unix was commonly used on minicomputers and mainframes from the 1970s onwards. It distinguished itself from its predecessors as the first portable operating system: almost the entire operating system is written in the C programming language (in 1973), which allows U ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Linux
Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, packaged as a Linux distribution (distro), which includes the kernel and supporting system software and library (computing), libraries—most of which are provided by third parties—to create a complete operating system, designed as a clone of Unix and released under the copyleft GPL license. List of Linux distributions, Thousands of Linux distributions exist, many based directly or indirectly on other distributions; popular Linux distributions include Debian, Fedora Linux, Linux Mint, Arch Linux, and Ubuntu, while commercial distributions include Red Hat Enterprise Linux, SUSE Linux Enterprise, and ChromeOS. Linux distributions are frequently used in server platforms. Many Linux distributions use the word "Linux" in their name, but the Free ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic Tree
A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics (also phylogeny inference) focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape. Phylogenetic trees may be rooted or unrooted. In a ''rooted'' p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bayes' Theorem
Bayes' theorem (alternatively Bayes' law or Bayes' rule, after Thomas Bayes) gives a mathematical rule for inverting Conditional probability, conditional probabilities, allowing one to find the probability of a cause given its effect. For example, if the risk of developing health problems is known to increase with age, Bayes' theorem allows the risk to someone of a known age to be assessed more accurately by conditioning it relative to their age, rather than assuming that the person is typical of the population as a whole. Based on Bayes' law, both the prevalence of a disease in a given population and the error rate of an infectious disease test must be taken into account to evaluate the meaning of a positive test result and avoid the ''base-rate fallacy''. One of Bayes' theorem's many applications is Bayesian inference, an approach to statistical inference, where it is used to invert the probability of Realization (probability), observations given a model configuration (i.e., th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Posterior Distribution
The posterior probability is a type of conditional probability that results from updating the prior probability with information summarized by the likelihood via an application of Bayes' rule. From an epistemological perspective, the posterior probability contains everything there is to know about an uncertain proposition (such as a scientific hypothesis, or parameter values), given prior knowledge and a mathematical model describing the observations available at a particular time. After the arrival of new information, the current posterior probability may serve as the prior in another round of Bayesian updating. In the context of Bayesian statistics, the posterior probability distribution usually describes the epistemic uncertainty about statistical parameters conditional on a collection of observed data. From a given posterior distribution, various point and interval estimates can be derived, such as the maximum a posteriori (MAP) or the highest posterior density interval ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Markov Chain Monte Carlo
In statistics, Markov chain Monte Carlo (MCMC) is a class of algorithms used to draw samples from a probability distribution. Given a probability distribution, one can construct a Markov chain whose elements' distribution approximates it – that is, the Markov chain's Discrete-time Markov chain#Stationary distributions, equilibrium distribution matches the target distribution. The more steps that are included, the more closely the distribution of the sample matches the actual desired distribution. Markov chain Monte Carlo methods are used to study probability distributions that are too complex or too highly N-dimensional space, dimensional to study with analytic techniques alone. Various algorithms exist for constructing such Markov chains, including the Metropolis–Hastings algorithm. General explanation Markov chain Monte Carlo methods create samples from a continuous random variable, with probability density proportional to a known function. These samples can be used to e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleotide
Nucleotides are Organic compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all Life, life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common Nutrient, nutrients by the liver. Nucleotides are composed of three subunit molecules: a nucleobase, a pentose, five-carbon sugar (ribose or deoxyribose), and a phosphate group consisting of one to three phosphates. The four nucleobases in DNA are guanine, adenine, cytosine, and thymine; in RNA, uracil is used in place of thymine. Nucleotides also play a central role in metabolism at a fundamental, cellular level. They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triph ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amino Acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 appear in the genetic code of life. Amino acids can be classified according to the locations of the core structural functional groups ( alpha- , beta- , gamma- amino acids, etc.); other categories relate to polarity, ionization, and side-chain group type ( aliphatic, acyclic, aromatic, polar, etc.). In the form of proteins, amino-acid '' residues'' form the second-largest component (water being the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. It is thought that they played a key role in enabling life on Earth and its emergence. Amino acids are formally named by the IUPAC- IUBMB Joint Commi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
