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1,400 | A ratite () is any of a diverse group of flightless, large, long-necked, and long-legged birds of the infraclass Palaeognathae. Kiwi, the exception, are much smaller and shorter-legged and are the only nocturnal extant ratites.
The systematics of and relationships within the paleognath clade have been in flux | Ratite |
1,401 | "Rauisuchia" is a paraphyletic group of mostly large and carnivorous Triassic archosaurs. Rauisuchians are a category of archosaurs within a larger group called Pseudosuchia, which encompasses all archosaurs more closely related to crocodilians than to birds and other dinosaurs. First named in the 1940s, Rauisuchia was a name exclusive to Triassic archosaurs which were generally large (often 4 to 6 metres (13 to 20 ft)), carnivorous, and quadrupedal with a pillar-erect hip posture, though exceptions exist for all of these traits | Rauisuchia |
1,402 | Reptiles, in common parlance, are a group of tetrapods with an ectothermic ('cold-blooded') metabolism and amniotic development. Living reptiles comprise four orders: Testudines (turtles), Crocodilia (crocodilians), Squamata (lizards and snakes), and Rhynchocephalia (the tuatara). As of May 2023, about 12,000 living species of reptiles are listed in the Reptile Database | Reptile |
1,403 | The Rhamphorhynchoidea forms one of the two suborders of pterosaurs and represents an evolutionary grade of primitive members of flying reptiles. This suborder is paraphyletic unlike the Pterodactyloidea, which arose from within the Rhamphorhynchoidea as opposed to a more distant common ancestor. Because it is not a completely natural grouping, Rhamphorhynchoidea is not used as a formal group in most scientific literature, though some pterosaur scientists continue to use it as an informal grouping in popular works, such as The Pterosaurs: From Deep Time by David Unwin, and in some formal studies | Rhamphorhynchoidea |
1,404 | Rhynchobdellida (from the Greek rhynchos, mouth, and bdellein, sucking), the jawless leeches or freshwater leeches, are an order of aquatic leeches. Despite the common name "freshwater leeches", species are found in both sea and fresh water. They are defined by the presence of a protrusible proboscis instead of jaws, and having colourless blood | Rhynchobdellida |
1,405 | "Roachoids", also known as "Roachids", "Blattoids" or Eoblattodea, are members of the stem group of Dictyoptera (the group containing modern cockroaches, termites and praying mantises). They generally resemble cockroaches, but most members, unlike modern dictyopterans, have generally long external ovipositors, and are thought not to have laid ootheca like modern dictyopterans.
Systematic position
Cockroaches are popularly thought to be an ancient order of insects, with their origins in the Carboniferous | Roachoid |
1,406 | Sauriurae (meaning "lizard tails" in Greek) is a now-deprecated subclass of birds created by Ernst Haeckel in 1866. It was intended to include Archaeopteryx and distinguish it from all other birds then known, which he grouped in the sister-group Ornithurae ("bird tails"). The distinction Haeckel referred to in this name is that Archaeopteryx possesses a long, reptile-like tail, while all other birds known to him had short tails with few vertebrae, fused at the end into a pygostyle | Sauriurae |
1,407 | Sawflies are the insects of the suborder Symphyta within the order Hymenoptera, alongside ants, bees, and wasps. The common name comes from the saw-like appearance of the ovipositor, which the females use to cut into the plants where they lay their eggs. The name is associated especially with the Tenthredinoidea, by far the largest superfamily in the suborder, with about 7,000 known species; in the entire suborder, there are 8,000 described species in more than 800 genera | Sawfly |
1,408 | Sea lions are pinnipeds characterized by external ear flaps, long foreflippers, the ability to walk on all fours, short and thick hair, and a big chest and belly. Together with the fur seals, they make up the family Otariidae, eared seals. The sea lions have six extant and one extinct species (the Japanese sea lion) in five genera | Sea lion |
1,409 | Silver dollar is a common name given to a number of species of fishes, mostly in the genus Metynnis, tropical fish belonging to the family Characidae which are closely related to piranha and pacu. Most commonly, the name refers to Metynnis argenteus. Native to South America, these somewhat round-shaped silver fish are popular with fish-keeping hobbyists | Silver dollar (fish) |
1,410 | Slug, or land slug, is a common name for any apparently shell-less terrestrial gastropod mollusc. The word slug is also often used as part of the common name of any gastropod mollusc that has no shell, a very reduced shell, or only a small internal shell, particularly sea slugs and semi slugs (this is in contrast to the common name snail, which applies to gastropods that have a coiled shell large enough that they can fully retract their soft parts into it).
Various taxonomic families of land slugs form part of several quite different evolutionary lineages, which also include snails | Slug |
1,411 | A snail is a shelled gastropod. The name is most often applied to land snails, terrestrial pulmonate gastropod molluscs. However, the common name snail is also used for most of the members of the molluscan class Gastropoda that have a coiled shell that is large enough for the animal to retract completely into | Snail |
1,412 | Soricomorpha (from Greek "shrew-form") is a formerly used taxon within the class of mammals. In the past it formed a significant group within the former order Insectivora. However, Insectivora was shown to be polyphyletic and various new orders were split off from it, including Afrosoricida (tenrecs, golden moles, otter shrews), Macroscelidea (elephant shrews), and Erinaceomorpha (hedgehogs and gymnures), with the four remaining extant and recent families of Soricomorpha shown here then being treated as a separate order | Soricomorpha |
1,413 | The Spheciformes is a paraphyletic assemblage of insect families which collectively comprise the "sphecoid wasps". Larvae are carnivorous.
These are all the members of the superfamily Apoidea, which are not bees and which in older classifications were called the "Sphecoidea" | Spheciformes |
1,414 | Sphenosuchia is a suborder of basal crocodylomorphs that first appeared in the Triassic and occurred into the Middle Jurassic. Most were small, gracile animals with an erect limb posture. They are now thought to be ancestral to crocodyliforms, a group which includes all living crocodilians | Sphenosuchia |
1,415 | The Stem Tetrapoda are a cladistically defined group, consisting of all animals more closely related to extant four-legged vertebrates than to their closest extant relatives (the lungfish), but excluding the crown group Tetrapoda. They are thus paraphyletic, though acceptable in phylogenetic nomenclature as the group is defined by strict reference to phylogeny rather than to traits as in traditional systematics. Thus, some finned sarcopterygians are considered to be stem tetrapods | Stem tetrapoda |
1,416 | Synziphosurina is a paraphyletic group of chelicerate arthropods previously thought to be basal horseshoe crabs (Xiphosura). It was later identified as a grade composed of various basal euchelicerates, eventually excluded form the monophyletic Xiphosura sensu stricto and only regarded as horseshoe crabs under a broader sense ('Xiphosura' sensu lato). Synziphosurines survived at least since early Ordovician to early Carboniferous in ages, with most species are known from the in-between Silurian strata | Synziphosurina |
1,417 | Tetra is the common name of many small freshwater characiform fishes. Tetras come from Africa, Central America, and South America, belonging to the biological family Characidae and to its former subfamilies Alestidae (the "African tetras") and Lebiasinidae. The Characidae are distinguished from other fish by the presence of a small adipose fin between the dorsal and caudal fins | Tetra |
1,418 | Thecodontia (meaning 'socket-teeth'), now considered an obsolete taxonomic grouping, was formerly used to describe a diverse "order" of early archosaurian reptiles that first appeared in the latest Permian period and flourished until the end of the Triassic period. All of them were built somewhat like crocodiles but with shorter skulls, more erect pose and usually somewhat lighter. The group includes the ancestors of dinosaurs, pterosaurs, and crocodilians, as well as a number of extinct forms that did not give rise to any descendants | Thecodontia |
1,419 | Tragulina (also known as Traguliformes) is an infraorder of even-toed ungulates. Only the chevrotains survive to the present, including the genera Tragulus (the mouse deer) and Hyemoschus, all within the family Tragulidae.
Taxonomy and Classification
Tragulina is an infraorder within the larger suborder Ruminantia, and is the sister clade to the infraorder Pecora | Tragulina |
1,420 | Triisodontidae is an extinct, probably paraphyletic, or possibly invalid family of mesonychian placental mammals. Most triisodontid genera lived during the Paleocene in North America, but the genus Andrewsarchus (if it is a mesonychian, and not an artiodactyl) is known from the middle Eocene of Asia. Triisodontids were the first relatively large predatory mammals to appear in North America following the extinction of the non-bird dinosaurs | Triisodontidae |
1,421 | The Turbellaria are one of the traditional sub-divisions of the phylum Platyhelminthes (flatworms), and include all the sub-groups that are not exclusively parasitic. There are about 4,500 species, which range from 1 mm (0. 039 in) to large freshwater forms more than 500 mm (20 in) long or terrestrial species like Bipalium kewense which can reach 600 mm (24 in) in length | Turbellaria |
1,422 | A wasp is any insect of the narrow-waisted suborder Apocrita of the order Hymenoptera which is neither a bee nor an ant; this excludes the broad-waisted sawflies (Symphyta), which look somewhat like wasps, but are in a separate suborder. The wasps do not constitute a clade, a complete natural group with a single ancestor, as bees and ants are deeply nested within the wasps, having evolved from wasp ancestors. Wasps that are members of the clade Aculeata can sting their prey | Wasp |
1,423 | Wastebasket taxon (also called a wastebin taxon, dustbin taxon or catch-all taxon) is a term used by some taxonomists to refer to a taxon that has the purpose of classifying organisms that do not fit anywhere else. They are typically defined by either their designated members' often superficial similarity to each other, or their lack of one or more distinct character states or by their not belonging to one or more other taxa. Wastebasket taxa are by definition either paraphyletic or polyphyletic, and are therefore not considered valid taxa under strict cladistic rules of taxonomy | Wastebasket taxon |
1,424 | Whales are a widely distributed and diverse group of fully aquatic placental marine mammals. As an informal and colloquial grouping, they correspond to large members of the infraorder Cetacea, i. e | Whale |
1,425 | White-fronted capuchin can refer to any of a number of species of gracile capuchin monkey which used to be considered as the single species Cebus albifrons. White-fronted capuchins are found in seven different countries in South America: Bolivia, Brazil, Colombia, Venezuela, Ecuador, Peru, and Trinidad and Tobago.
White-fronted capuchins are medium-sized monkeys with a light brown back and a creamy white underside | White-fronted capuchin |
1,426 | Wobblata is a paraphyletic grouping of all placidozoans except Opalinata. It unites the classes Placididea, Nanomonadea and Opalomonadea.
Description
Members of this group are ancestrally aerobic phagotrophic biciliates | Wobblata |
1,427 | Younginiformes is a replacement name for the taxon Eosuchia, proposed by Alfred Romer in 1947.
The Eosuchia having become a wastebasket taxon for many probably distantly-related primitive diapsid reptiles ranging from the late Carboniferous to the Eocene, Romer proposed that this be replaced by Younginiformes, to include the Younginidae and a very few similar families, ranging from the Permian to the Triassic.
Younginiformes (including Acerosodontosaurus, Hovasaurus, Kenyasaurus, Tangasaurus, Thadeosaurus, Youngina, et alia sensu Currie and other researchers in the 1980s) is probably not a clade | Younginiformes |
1,428 | Algae (UK: , US: ; SG: alga ) is an informal term for a large and diverse group of photosynthetic, eukaryotic organisms. It is a polyphyletic grouping that includes species from multiple distinct clades. Included organisms range from unicellular microalgae, such as Chlorella, Prototheca and the diatoms, to multicellular forms, such as the giant kelp, a large brown alga which may grow up to 50 metres (160 ft) in length | Algae |
1,429 | The term antelope is used to refer to a number of species of ruminant artiodactyls—i. e. , multiple-stomached, cud-chewing, even-toed hoofed mammals—that are indigenous to most of Africa, India, the Middle East, Central Asia, and a small area of Eastern Europe | Antelope |
1,430 | Birds of prey or predatory birds, also known as raptors, are hypercarnivorous bird species that actively hunt and feed on other vertebrates (mainly mammals, reptiles and other smaller birds). In addition to speed and strength, these predators have keen eyesight for detecting prey from a distance or during flight, strong feet with sharp talons for grasping or killing prey, and powerful, curved beaks for tearing off flesh. Although predatory birds primarily hunt live prey, many species (such as fish eagles, vultures and condors) also scavenge and eat carrion | Bird of prey |
1,431 | Brain coral is a common name given to various corals in the families Mussidae and Merulinidae, so called due to their generally spheroid shape and grooved surface which resembles a brain. Each head of coral is formed by a colony of genetically identical polyps which secrete a hard skeleton of calcium carbonate; this makes them important coral reef builders like other stony corals in the order Scleractinia.
Brain corals are found in shallow warm water coral reefs in all the world's oceans | Brain coral |
1,432 | Coxsackieviruses are a few related enteroviruses that belong to the Picornaviridae family of nonenveloped, linear, positive-sense single-stranded RNA viruses, as well as its genus Enterovirus, which also includes poliovirus and echovirus. Enteroviruses are among the most common and important human pathogens, and ordinarily its members are transmitted by the fecal–oral route. Coxsackieviruses share many characteristics with poliovirus | Coxsackievirus |
1,433 | The Drosophila immigrans species group is a polyphyletic and speciose lineage of Drosophila flies, including over 100 species. Immigrans species belong to the Immigrans-tripunctata radiation of the subgenus Drosophila. Well-described species include Drosophila immigrans, and the sister species Drosophila albomicans and Drosophila nasuta | Drosophila immigrans species group |
1,434 | Dung beetles are beetles that feed on feces. Some species of dung beetles can bury dung 250 times their own mass in one night. Many dung beetles, known as rollers, roll dung into round balls, which are used as a food source or breeding chambers | Dung beetle |
1,435 | An endotherm (from Greek ἔνδον endon "within" and θέρμη thermē "heat") is an organism that maintains its body at a metabolically favorable temperature, largely by the use of heat released by its internal bodily functions instead of relying almost purely on ambient heat. Such internally generated heat is mainly an incidental product of the animal's routine metabolism, but under conditions of excessive cold or low activity an endotherm might apply special mechanisms adapted specifically to heat production. Examples include special-function muscular exertion such as shivering, and uncoupled oxidative metabolism, such as within brown adipose tissue | Endotherm |
1,436 | The Entognatha are a class of wingless and ametabolous arthropods, which, together with the insects, makes up the subphylum Hexapoda. Their mouthparts are entognathous, meaning that they are retracted within the head, unlike the insects. Entognatha are apterous, meaning that they lack wings | Entognatha |
1,437 | Euryapsida is a polyphyletic (unnatural, as the various members are not closely related) group of sauropsids that are distinguished by a single temporal fenestra, an opening behind the orbit, under which the post-orbital and squamosal bones articulate. They are different from Synapsida, which also have a single opening behind the orbit, by the placement of the fenestra. In synapsids, this opening is below the articulation of the post-orbital and squamosal bones | Euryapsida |
1,438 | The order Insectivora (from Latin insectum "insect" and vorare "to eat") is a now-abandoned biological grouping within the class of mammals. Some species have now been moved out, leaving the remaining ones in the order Eulipotyphla within the larger clade Laurasiatheria, which makes up one of the basal clades of placental mammals.
History
Before the era of widespread DNA sequencing, the grouping was used as a polyphyletic taxon for a variety of small to very small, relatively unspecialised mammals that feed upon insects | Insectivora |
1,439 | Lepospondyli is a diverse taxon of early tetrapods. With the exception of one late-surviving lepospondyl from the Late Permian of Morocco (Diplocaulus minumus), lepospondyls lived from the Early Carboniferous (Mississippian) to the Early Permian and were geographically restricted to what is now Europe and North America. Five major groups of lepospondyls are known: Adelospondyli; Aïstopoda; Lysorophia; Microsauria; and Nectridea | Lepospondyli |
1,440 | Limpets are a group of aquatic snails that exhibit a conical shell shape (patelliform) and a strong, muscular foot. Limpets are members of the class Gastropoda, but are polyphyletic, meaning the various groups called "limpets" descended independently from different ancestral gastropods. This general category of conical shell is known as "patelliform" (dish-shaped) | Limpet |
1,441 | Lipotyphla is a formerly used order of mammals, including the members of the order Eulipotyphla (i. e. the solenodons, family Solenodontidae; hedgehogs and gymnures, family Erinaceidae; desmans, moles, and shrew-like moles, family Talpidae; and true shrews, family Soricidae) as well as three other families of the former order Insectivora, Chrysochloridae (golden moles), Tenrecidae (tenrecs), and Potamogalidae (otter shrews) | Lipotyphla |
1,442 | Microlepidoptera (micromoths) is an artificial (i. e. , unranked and not monophyletic) grouping of moth families, commonly known as the "smaller moths" (micro, Lepidoptera) | Microlepidoptera |
1,443 | Monodnaviria is a realm of viruses that includes all single-stranded DNA viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication of the circular viral genome. Viruses descended from such viruses are also included in the realm, including certain linear single-stranded DNA (ssDNA) viruses and circular double-stranded DNA (dsDNA) viruses. These atypical members typically replicate through means other than rolling circle replication | Monodnaviria |
1,444 | Ostracoderms (lit. 'shell-skins') are the armored jawless fish of the Paleozoic Era. The term does not often appear in classifications today because it is paraphyletic (excluding jawed fishes) (may also be polyphyletic if anaspids are closer to cyclostomes) and thus does not correspond to one evolutionary lineage | Ostracoderm |
1,445 | The phylum Sarcomastigophora belongs to the Protista or protoctista kingdom and it includes many unicellular or colonial, autotrophic, or heterotrophic organisms. It is characterized by flagella, pseudopodia, or both.
Taxonomy
It is divided into three subphyla: the Mastigophora, the Sarcodina and the Opalinata | Sarcomastigophora |
1,446 | Seaweed, or macroalgae, refers to thousands of species of macroscopic, multicellular, marine algae. The term includes some types of Rhodophyta (red), Phaeophyta (brown) and Chlorophyta (green) macroalgae. Seaweed species such as kelps provide essential nursery habitat for fisheries and other marine species and thus protect food sources; other species, such as planktonic algae, play a vital role in capturing carbon, producing at least 50% of Earth's oxygen | Seaweed |
1,447 | Stenopterygii are a superorder of ray-finned fish in the infraclass Teleostei. Their validity is somewhat doubtful, as the group was established to separate, out of a large group of closely related Teleostei, a mere two rather peculiarly autapomorphic orders at best. In some treatments, it is even monotypic | Stenopterygii |
1,448 | The Thermoanaerobacterales is a polyphyletic order of bacteria placed within the polyphyletic class Clostridia, and encompassing four families: the Thermoanaerobacteraceae, the Thermodesulfobiaceae, the Thermoanaerobacterales Family III. Incertae Sedis, and the Thermoanaerobacterales Family IV. Incertae Sedis, and various unplaced genera | Thermoanaerobacterales |
1,449 | Trachiniformes is an order of percomorph bony fish, whose contents are traditionally pllaced in suborder Trachinoidei of Perciformes. However, Trachiniformes is recovered as polyphyletic in recent large scale molecular phylogenetic studies. Trachinidae itself is recovered as part of Percoidei, while other families respectively belong to Scombriformes, Gobiiformes, new orders Uranoscopiformes and Pempheriformes, and other clades in Perciformes | Trachiniformes |
1,450 | Turrid, plural turrids, is a common name for a very large group of predatory sea snails, marine gastropod mollusks which until recently were all classified in the family Turridae. However, recently the family was discovered to be polyphyletic and therefore was split into a number of families.
The original family Turridae used to contain more than 4,000 species | Turrid |
1,451 | A vulture is a bird of prey that scavenges on carrion. There are 23 extant species of vulture (including Condors). Old World vultures include 16 living species native to Europe, Africa, and Asia; New World vultures are restricted to North and South America and consist of seven identified species, all belonging to the Cathartidae family | Vulture |
1,452 | Wastebasket taxon (also called a wastebin taxon, dustbin taxon or catch-all taxon) is a term used by some taxonomists to refer to a taxon that has the purpose of classifying organisms that do not fit anywhere else. They are typically defined by either their designated members' often superficial similarity to each other, or their lack of one or more distinct character states or by their not belonging to one or more other taxa. Wastebasket taxa are by definition either paraphyletic or polyphyletic, and are therefore not considered valid taxa under strict cladistic rules of taxonomy | Wastebasket taxon |
1,453 | The witchetty grub (also spelled witchety grub or witjuti grub) is a term used in Australia for the large, white, wood-eating larvae of several moths. In particular, it applies to the larvae of the cossid moth Endoxyla leucomochla, which feeds on the roots of the witchetty bush (after which the grubs are named) that is widespread throughout the Northern Territory and also typically found in parts of Western Australia and South Australia, although it is also found elsewhere throughout Australia.
The term may also apply to larvae of other cossid moths, ghost moths (Hepialidae), and longhorn beetles (Cerambycidae) | Witchetty grub |
1,454 | This page is a subsection of the list of sequence alignment software.
Multiple alignment visualization tools typically serve four purposes:
Aid general understanding of large-scale DNA or protein alignments
Visualize alignments for figures and publication
Manually edit and curate automatically generated alignments
Analysis in depthThe rest of this article is focused on only multiple global alignments of homologous proteins. The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature | List of alignment visualization software |
1,455 | Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry.
Proteomics software
In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS2) experiments are used for protein/peptide identification. Peptide identification algorithms fall into two broad classes: database search and de novo search | List of mass spectrometry software |
1,456 | This is a list of notable software systems that are used for visualizing macromolecules.
Key
The tables below indicate which types of data can be visualized in each system:
See also
Biological data visualization
Comparison of nucleic acid simulation software
Comparison of software for molecular mechanics modeling
List of microscopy visualization systems
List of open-source bioinformatics software
Molecular graphics
Molecule editor
References
External links
Saric M. "Free Molecular Modelling Programs =" | List of molecular graphics systems |
1,457 | This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Methods for estimating phylogenies include neighbor-joining, maximum parsimony (also simply referred to as parsimony), UPGMA, Bayesian phylogenetic inference, maximum likelihood and distance matrix methods | List of phylogenetics software |
1,458 | Systems biology relies heavily on building mathematical models to help understand and make predictions of biological processes. Specialized software to assist in building models has been developed since the arrival of the first digital computers. The following list gives the currently supported software applications available to researchers | List of systems biology modeling software |
1,459 | Ambra Health (formerly DICOM Grid), is a software company that provides solutions for medical image sharing of DICOM and non-DICOM data between patients, physicians, and hospitals.
History
The company was founded as DICOM Grid, Inc. in 2004 to make digital medical imaging on a cloud based platform | Ambra Health |
1,460 | Digital Imaging and Communications in Medicine (DICOM) is the standard for the communication and management of medical imaging information and related data. DICOM is most commonly used for storing and transmitting medical images enabling the integration of medical imaging devices such as scanners, servers, workstations, printers, network hardware, and picture archiving and communication systems (PACS) from multiple manufacturers. It has been widely adopted by hospitals and is making inroads into smaller applications such as dentists' and doctors' offices | DICOM |
1,461 | DICOMweb is a term applied to the family of RESTful DICOM services defined for sending, retrieving and querying for medical images and related information.
The intent is to provide a light-weight mobile device and web browser friendly mechanism for accessing images, which can be implemented by developers who have minimal familiarity with the DICOM standard and which uses consumer application friendly mechanisms like http, JSON and media types (like "image/jpeg") to the maximum extent possible.
The standard is formally defined in DICOM PS3 | DICOMweb |
1,462 | OsiriX is an image processing application for the Apple MacOS operating system dedicated to DICOM images (". dcm" / ". DCM" extension) produced by equipment (MRI, CT, PET, PET-CT, | OsiriX |
1,463 | VistA Imaging is an FDA-listed Image Management system used in the Department of Veterans Affairs healthcare facilities nationwide. It is one of the most widely used image management systems in routine healthcare use, and is used to manage many different varieties of images associated with a patient's medical record. The system was started as a research project by Ruth Dayhoff in 1986 and was formally launched in 1991 | VistA Imaging |
1,464 | AMPHORA ("AutoMated Phylogenomic infeRence Application") is an open-source bioinformatics workflow. AMPHORA2 uses 31 bacterial and 104 archaeal phylogenetic marker genes for inferring phylogenetic information from metagenomic datasets. Most of the marker genes are single copy genes, therefore AMPHORA2 is suitable for inferring the accurate taxonomic composition of bacterial and archaeal communities from metagenomic shotgun sequencing data | AMPHORA |
1,465 | The AMRFinderPlus tool from the National Center for Biotechnology Information (NCBI) is a bioinformatic tool that allows users to identify antimicrobial resistance determinants, stress response, and virulence genes in bacterial genomes. This tool's development began in 2018 (as AMRFinder) and is still underway. The National Institutes of Health funds the development of the software and the databases it uses | AMRFinderPlus |
1,466 | Apache cTAKES: clinical Text Analysis and Knowledge Extraction System is an open-source Natural Language Processing (NLP) system that extracts clinical information from electronic health record unstructured text. It processes clinical notes, identifying types of clinical named entities — drugs, diseases/disorders, signs/symptoms, anatomical sites and procedures. Each named entity has attributes for the text span, the ontology mapping code, context (family history of, current, unrelated to patient), and negated/not negated | Apache cTAKES |
1,467 | Arlequin is a free population genetics software distributed as an integrated GUI data analysis software. It performs several types of tests and calculations, including Fixation index (Fst, also known as the "F-statistics"), computing genetic distance, Hardy–Weinberg equilibrium, linkage disequilibrium, analysis of molecular variance, mismatch distribution, and pairwise difference tests. The software is designed to be able to handle different kinds of molecular, non-molecular, and/or frequency type data | Arlequin (software) |
1,468 | The Bioclipse project is a Java-based, open-source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). It gained scripting functionality in 2009, and a command line version in 2021. Like any RCP application, Bioclipse uses a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc | Bioclipse |
1,469 | Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.
Bioconductor is based primarily on the statistical R programming language, but does contain contributions in other programming languages. It has two releases each year that follow the semiannual releases of R | Bioconductor |
1,470 | BioJS is an open-source project for bioinformatics data on the web. Its goal is to develop an open-source library of JavaScript components to visualise biological data. BioJS develops and maintains small building blocks (components) which can be reused by others | BioJS |
1,471 | BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project.
Background
BioPerl is an active open source software project supported by the Open Bioinformatics Foundation | BioPerl |
1,472 | BioPHP is a collection of open-source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools. BioRuby is released under the GNU GPL version 2 licence and is one of a number of Bio* projects, designed to reduce code duplication. As an open source bioinformatics project, BioPHP is affiliated with the Open Bioinformatics Foundation | BioPHP |
1,473 | BioRuby is a collection of open-source Ruby code, comprising classes for computational molecular biology and bioinformatics. It contains classes for DNA and protein sequence analysis, sequence alignment, biological database parsing, structural biology and other bioinformatics tasks. BioRuby is released under the GNU GPL version 2 or Ruby licence and is one of a number of Bio* projects, designed to reduce code duplication | BioRuby |
1,474 | GenoCAD is one of the earliest computer assisted design tools for synthetic biology. The software is a bioinformatics tool developed and maintained by GenoFAB, Inc. | GenoCAD |
1,475 | GenomeSpace is an environment for genomics software tools and applications. It helps users manage their analysis workflows involving multiple diverse tools, including web applications and desktop tools and facilitates the transfer of data between tools via automatic format conversion. Analyses can use data from local or cloud-based stores | Genomespace |
1,476 | The Genomic HyperBrowser is a web-based system for statistical analysis of genomic annotation data.
History
The Genomic HyperBrowser has been developed since early 2008 and went public in December 2010. The latest version of the system (v1 | The Genomic HyperBrowser |
1,477 | Integrated Genome Browser (IGB) (pronounced Ig-Bee) is an open-source genome browser, a visualization tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.
History
Integrated Genome Browser was first developed at Affymetrix for their scientists and public sector collaborators to visualize data from genome-wide tiling arrays. The first iterations of IGB were developed using funding from NIH awarded to company scientists Gregg Helt and Tom Gingeras | Integrated Genome Browser |
1,478 | KNIME (), the Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks of Analytics" concept. A graphical user interface and use of JDBC allows assembly of nodes blending different data sources, including preprocessing (ETL: Extraction, Transformation, Loading), for modeling, data analysis and visualization without, or with only minimal, programming | KNIME |
1,479 | LabKey Server is a software suite available for scientists to integrate, analyze, and share biomedical research data. The platform provides a secure data repository that allows web-based querying, reporting, and collaborating across a range of data sources. Specific scientific applications and workflows can be added on top of the basic platform and leverage a data processing pipeline | LabKey Server |
1,480 | Mega2 (short for manipulation environment for genetic analysis) allows the applied statistical geneticist to convert one's data from several input formats to a large number output formats suitable for analysis by commonly used software packages. In a typical human genetics study, the analyst often needs to use a variety of different software programs to analyze the data, and these programs usually require that the data be formatted to their precise input specifications. Conversion of one's data into these multiple different formats can be tedious, time-consuming, and error-prone | Mega2, the Manipulation Environment for Genetic Analysis |
1,481 | mothur is an open source software package for bioinformatics data processing. The package is frequently used in the analysis of DNA from uncultured microbes. mothur is capable of processing data generated from several DNA sequencing methods including 454 pyrosequencing, Illumina HiSeq and MiSeq, Sanger, PacBio, and IonTorrent | Mothur |
1,482 | PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways.
Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible | PathVisio |
1,483 | AMPHORA ("AutoMated Phylogenomic infeRence Application") is an open-source bioinformatics workflow. AMPHORA2 uses 31 bacterial and 104 archaeal phylogenetic marker genes for inferring phylogenetic information from metagenomic datasets. Most of the marker genes are single copy genes, therefore AMPHORA2 is suitable for inferring the accurate taxonomic composition of bacterial and archaeal communities from metagenomic shotgun sequencing data | AMPHORA |
1,484 | CAMERA, or the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis, is an online cloud computing service that provides hosted software tools and a high-performance computing infrastructure for the analysis of metagenomic data. The project was announced in January 2006, becoming Calit2's flagship project.
Mission
The project aims to accelerate genomic research by amassing a large repository of metagenomic data generated by independent members of the research community at large, by developing a custom bioinformatics toolset optimized for cluster computing, and by offering the high-performance computing infrastructure on which to run it | Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis |
1,485 | De novo sequence assemblers are a type of program that assembles short nucleotide sequences into longer ones without the use of a reference genome. These are most commonly used in bioinformatic studies to assemble genomes or transcriptomes. Two common types of de novo assemblers are greedy algorithm assemblers and De Bruijn graph assemblers | De novo sequence assemblers |
1,486 | GeneMark is a generic name for a family of ab initio gene prediction programs developed at the Georgia Institute of Technology in Atlanta. Developed in 1993, original GeneMark was used in 1995 as a primary gene prediction tool for annotation of the first completely sequenced bacterial genome of Haemophilus influenzae, and in 1996 for the first archaeal genome of Methanococcus jannaschii. The algorithm introduced inhomogeneous three-periodic Markov chain models of protein-coding DNA sequence that became standard in gene prediction as well as Bayesian approach to gene prediction in two DNA strands simultaneously | GeneMark |
1,487 | MEGAN ("MEtaGenome ANalyzer") is a computer program that allows optimized analysis of large metagenomic datasets. Metagenomics is the analysis of the genomic sequences from a usually uncultured environmental sample. A large term goal of most metagenomics is to inventory and measure the extent and the role of microbial biodiversity in the ecosystem due to discoveries that the diversity of microbial organisms and viral agents in the environment is far greater than previously estimated | MEGAN |
1,488 | SPAdes (St. Petersburg genome assembler) is a genome assembly algorithm which was designed for single cell and multi-cells bacterial data sets. Therefore, it might not be suitable for large genomes projects | SPAdes (software) |
1,489 | UniFrac is a distance metric used for comparing biological communities. It differs from dissimilarity measures such as Bray-Curtis dissimilarity in that it incorporates information on the relative relatedness of community members by incorporating phylogenetic distances between observed organisms in the computation.
Both weighted (quantitative) and unweighted (qualitative) variants of UniFrac are widely used in microbial ecology, where the former accounts for abundance of observed organisms, while the latter only considers their presence or absence | UniFrac |
1,490 | Velvet is an algorithm package that has been designed to deal with de novo genome assembly and short read sequencing alignments. This is achieved through the manipulation of de Bruijn graphs for genomic sequence assembly via the removal of errors and the simplification of repeated regions. Velvet has also been implemented in commercial packages, such as Sequencher, Geneious, MacVector and BioNumerics | Velvet assembler |
1,491 | Neuroimaging software is used to study the structure and function of the brain. To see an NIH Blueprint for Neuroscience Research funded clearinghouse of many of these software applications, as well as hardware, etc. go to the NITRC web site | List of neuroimaging software |
1,492 | The AIR (Automated Image Registration) is a program suite for volume-based image registration constructed by Roger P. Woods from UCLA School of Medicine.
It reads and writes Analyze volume files and can work with 4x4 transformation matrices stored in its own file format with the filename extension | AIR (program) |
1,493 | Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying functional MRI data—a technique for mapping human brain activity.
AFNI is an agglomeration of programs that can be used interactively or flexibly assembled for batch processing using shell script. The term AFNI refers both to the entire suite and to a particular interactive program often used for visualization | Analysis of Functional NeuroImages |
1,494 | Analyze is a software package developed by the Biomedical Imaging Resource (BIR) at Mayo Clinic for multi-dimensional display, processing, and measurement of multi-modality biomedical images. It is a commercial program and is used for medical tomographic scans from magnetic resonance imaging, computed tomography and positron emission tomography.
The Analyze 7 | Analyze (imaging software) |
1,495 | Cambridge Brain Analysis (CamBA), is a software repository developed at the Brain Mapping Unit, Department of Psychiatry, University of Cambridge, UK and contains software pipelines for functional magnetic resonance imaging (fMRI) analysis. It is designed for batch processing and its main graphical user interface offers a spreadsheet-like look-and-feel.
The software is available under the GNU General Public License and runs under Linux | Cambridge Brain Analysis |
1,496 | CARET (Computerized Anatomical Reconstruction Toolkit) is a software application for the structural and functional analysis of the cerebral and cerebellar cortex. CARET is developed in the Van Essen Laboratory in the Department of Anatomy and Neurobiology at the Washington University School of Medicine in St. Louis, Missouri | Caret (software) |
1,497 | CONN is a Matlab-based cross-platform imaging software for the computation, display, and analysis of functional connectivity in fMRI (functional Magnetic Resonance Imaging) in the resting state and during task.
CONN is available as an SPM toolbox, as well as precompiled binaries for MacOS/Windows/Linux environments, and it is freely available for non-commercial use.
Functionality
CONN includes a user-friendly GUI to manage all aspects of functional connectivity analyses, including preprocessing of functional and anatomical volumes, elimination of subject-movement and physiological noise, outlier scrubbing, estimation of multiple connectivity and network measures, and population-level hypothesis testing | CONN (functional connectivity toolbox) |
1,498 | The Dextroscope is a medical equipment system that creates a virtual reality (VR) environment in which surgeons can plan neurosurgical and other surgical procedures. The Dextroscope is designed to show a patient's 3D anatomical relationships and pathology in great detail. Although its main purpose is for planning surgery, the dextroscope has also proven useful in research in cardiology, radiology and medical education | Dextroscope |
1,499 | Fiji (Fiji Is Just ImageJ) is an open source image processing package based on ImageJ2.
Fiji's main purpose is to provide a distribution of ImageJ2 with many bundled plugins. Fiji features an integrated updating system and aims to provide users with a coherent menu structure, extensive documentation in the form of detailed algorithm descriptions and tutorials, and the ability to avoid the need to install multiple components from different sources | Fiji (software) |
Subsets and Splits