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Bioinformatics technique
Phylogenetic profiling is a bioinformatics technique in which the joint presence or joint absence of two traits across large numbers of species is used
Phylogenetic_profiling
Study of evolutionary relationships between organisms
In biology, phylogenetics (/ˌfaɪloʊdʒəˈnɛtɪks, -lə-/) is the study of the evolutionary history of life using observable characteristics of organisms (or
Phylogenetics
Prediction by observation and computation
database (JGI IMG) that has a phylogenetic profiling tool for single genes and gene cassettes. It was observed that the phylogenetic trees of ligands and receptors
Protein–protein interaction prediction
Protein–protein_interaction_prediction
The Nucleic acid phylogenetic profiling (NAPP) is a database of coding and non-coding sequences according to their pattern of conservation across the other
NAPP_(database)
deviations from the genomic average whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly
Inferring horizontal gene transfer
Inferring_horizontal_gene_transfer
RNA family
aureus N315 using a large-scale computational screening based on phylogenetic profiling. It was first identified, but not named, in 2005. RsaOG has since
RsaOG
Protein domain
metabolism proteins which are homologous to eukaryotic frataxin. Partial phylogenetic profiling suggests that CyaY most likely functions as part of the ISC system
Frataxin-like_domain
Family of integral membrane proteins
environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic". BMC Biology. 4 29. doi:10.1186/1741-7007-4-29. PMC 1569441
Exosortase
Measure of dependence between two variables
secondary structure prediction from a multiple sequence alignment. Phylogenetic profiling prediction from pairwise present and disappearance of functionally
Mutual_information
Field of study
Microbial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution
Microbial_phylogenetics
Physical interactions and constructions between multiple proteins
interaction types, etc.) is extracted. There are also studies using phylogenetic profiling, basing their functionalities on the theory that proteins involved
Protein–protein_interaction
Use of bioinformatic methods to correlate proteins with biofunctions
the local genomic or phylogenomic context and structure of genes: Phylogenetic profiling is based on the observation that two or more proteins with the same
Protein_function_prediction
Organisms capable of living in extreme environments
M, Pal KK, Dey R, Gupta A, et al. (31 May 2014). "Diversity and phylogenetic profiling of niche-specific Bacilli from extreme environments of India". Annals
Extremophile
identifying functional interactions between proteins, including phylogenetic profiling, Rosetta Stone gene fusion, mRNA coexpression, and mirror tree approaches
Edward_Marcotte
This list of phylogenetic tree viewing software is a compilation of software tools and web portals used in visualizing phylogenetic trees. 1 "All" refers
List of phylogenetic tree visualization software
List_of_phylogenetic_tree_visualization_software
Protein–protein interactions in human cells
potential interactions predicted from interactome data, whether through phylogenetic profiling (evolutionary similarity), statistical network inference, or text/literature
Human_interactome
Species of wasp
moisture diffusion, so prevent dehydration in wasps. Cuticular hydrocarbon profiles vary over species and nests, and they are a proposed mechanism for nest-mate
Dolichovespula_maculata
American computer scientist
alignment, and phylogenetic placement. This work includes TIPP3, which was shown to provide improved accuracy for abundance profiling, and TIPP-SD, which
Tandy_Warnow
Species of bacterium
safensis but also some B. pumilus strains, thus suggesting how phylogenetic profiling may enable re-examining the strain designations. Listed below are
Bacillus_safensis
Similar DNA, RNA or protein sequences within genomes or among species
sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time. Examples of highly conserved
Conserved_sequence
Biological database
same metabolic pathway, must be expressed together and have similar phylogenetic profile. Coexpression: Predicted association between genes based on observed
STRING
classification of all noncoding sequences in a bacterial genome using phylogenetic profiles". Genome Research. 19 (6): 1084–1092. doi:10.1101/gr.089714.108
Rsa_RNA
Type of virus that infects the domain of unicellular, prokaryotic organisms or Archaea
PMID 26459284. S2CID 17018998. Huang L, Wang H (March 2021). "ICTV Virus Taxonomy Profile: Ovaliviridae". J Gen Virol. 102 (3). doi:10.1099/jgv.0.001546. PMC 8515868
Archaeal_virus
Earth's most severe extinction event
zones. Brachiopod taxa during the Anisian recovery interval were only phylogenetically related to Late Permian brachiopods at a familial taxonomic level or
Permian–Triassic extinction event
Permian–Triassic_extinction_event
Species of bacterium
based on information obtained from 16S rRNA gene sequence analysis. Phylogenetic studies revealed that the organism was genetically distinct from other
Acidithiobacillus ferrooxidans
Acidithiobacillus_ferrooxidans
Passerine bird native to Australia
taxonomic evaluation of the waxbills (Aves: Estrildidae)". Molecular Phylogenetics and Evolution. 146 106757. Bibcode:2020MolPE.14606757O. doi:10.1016/j
Gouldian_finch
Tribe of birds
ISSN 1175-5334. Forshaw, Joseph Michael (2017). Vanished and vanishing parrots : profiling extinct and endangered species. Illustrated by Frank Knight. Collingwood:
Fig_parrot
Technique in evolutionary study
that a phylogenetic tree representing the evolution of an entity (e.g. homologous genes or symbionts) can be drawn within another phylogenetic tree representing
Phylogenetic_reconciliation
Country in Southeastern Europe and West Asia
246 Beckman 2012, p. 522 Heggarty, Paul (2021). "Cognacy Databases and Phylogenetic Research on Indo-European". Annual Review of Linguistics. 7: 371–394
Turkey
Highly polymorphic DNA region
1007/s00239-010-9377-4. PMID 20700734. S2CID 1424625. Carracedo A. "DNA Profiling". Archived from the original on 27 September 2001. Retrieved 20 September
Hypervariable_region
Topics referred to by the same term
(1916–1993), American baseball umpire NAPP (database) (Nucleic Acid Phylogenetic Profile Database) National Association of Patent Practitioners National Association
Napp
Type of psychoactive fungus
Nian-Kai; Hosen, Md. Iqbal; Yang, Zhu L. (November 2014). "Molecular phylogenetic analyses redefine seven major clades and reveal 22 new generic clades
Hallucinogenic bolete mushroom
Hallucinogenic_bolete_mushroom
New Zealand scientist
The title of his 2008 doctoral thesis is The archives of history: a phylogenetic approach to the study of language. Greenhill is currently a scientist
Simon_Greenhill
Open-access database for Y chromosome variations
structured to display the geographic, linguistic and phylogenetic relationship of searched haplotype profiles. Currently the YHRD database recognizes four separate
Y Chromosome Haplotype Reference Database
Y_Chromosome_Haplotype_Reference_Database
Species of bacterium
within the class Clostridia, following reclassification based on the phylogenetic and 16S rRNA gene analyses that distinguished it from earlier Ruminococcacae
Mediterraneibacter_gnavus
Virus that causes COVID-19
sufficient number of sequenced genomes, it is possible to reconstruct a phylogenetic tree of the mutation history of a family of viruses. By 12 January 2020
SARS-CoV-2
Species of great ape
(2015). "Primate Phylogenetic Relationships and Divergence Dates Inferred from Complete Mitochondrial Genomes". Molecular Phylogenetics and Evolution. 75:
Chimpanzee
Chinese historical period
first enabled the dating of this ancient migration: Lapita. According to phylogenetic research on Austronesian languages, these populations are believed to
Neolithic_in_China
Species of roundworm
(grey box). The image below shows more detailed information about the phylogenetic tree of M. composticola Steel H, Moens T, Scholaert A, Boshoff M, Houthoofd
Mononchoides_composticola
Protein-coding gene in the species Homo sapiens
et al. (April 2020). "Syncytiotrophoblast extracellular microvesicle profiles in maternal circulation for noninvasive diagnosis of preeclampsia". Scientific
Placenta-specific_protein_1
Genus of trees and shrubs
type species: Prunus laurocerasus (European cherry-laurel) An extensive phylogenetic study based on different chloroplast and nuclear sequences divides Prunus
Prunus
Class of chemical compounds
PMID 19456333. S2CID 6304998. Elphick, M. R.; Egertová, M. (2005), "The Phylogenetic Distribution and Evolutionary Origins of Endocannabinoid Signalling"
N-Acylethanolamine
Species of bird
formerly placed in the genus Accipiter. In 2024 a comprehensive molecular phylogenetic study of the Accipitridae confirmed earlier work that had shown that
Cooper's_hawk
Salamander in the subfamily Pleurodelinae
exclusively functional term for salamanders living in water, and not a clade. Phylogenetic analyses have however shown that species in the Salamandridae traditionally
Newt
Yellow citrus fruit
Andres; Luro, François; Navarro, Luis; Ollitrault, Patrick (2016). "Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers"
Lemon
Largest species of toothed whale
PMID 16094808. Montgelard, C.; Catzeflis, FM.; Douzery, E. (1997). "Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison
Sperm_whale
Human Y-chromosome DNA haplogroup
Mengge; Hu, Liping; He, Guanglin; Nie, Shengjie (May 2024). "Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern
Haplogroup_NO1
Species of legume
Germplasm Resources Information Network. Agricultural Research Service, United States Department of Agriculture. Jepson Manual Treatment USDA Plants Profile
Senna_didymobotrya
professor of paleontology, researcher in vertebrate paleontology, phylogenetics and biogeography Tracy Ainsworth, marine biologist and coral reef expert
List of University of New South Wales faculty
List_of_University_of_New_South_Wales_faculty
Species of bear native to the Arctic
(2007). "Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid
Polar_bear
Subspecies of brown bear
identified by a "dished in" profile of their face with short, rounded ears, whereas a black bear has a straight face profile and longer ears. A grizzly
Grizzly_bear
Family of carnivoran mammals
are unique and vital components of most African ecosystems. Although phylogenetically closer to felines and viverrids, hyenas are behaviourally and morphologically
Hyena
Characteristic of a group of organisms with a common ancestor
modern archaea also. Another important piece of evidence is from detailed phylogenetic trees (i.e., "genealogic trees" of species) mapping out the proposed
Common_descent
Genus of trees in the family Fagaceae
PMC 8921187. PMID 35288565. Manos, Paul S.; Steele, Kelly P. (1997). "Phylogenetic analysis of "Higher" Hamamelididae based on Plasid Sequence Data". American
Beech
Bioinformatics software package
is a bioinformatics software package. The name is an abbreviation for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.
PICRUSt
Family of reptiles
particular, placental development of whatever degree in lizards is phylogenetically analogous, rather than homologous, to functionally similar processes
Skink
Species of bacteria
but was reclassified in 2020 to the Phocaeicola genus. This was due to phylogenetic analysis suggesting it to be more closely related to the Phocaeicola
Phocaeicola_vulgatus
Species of snake
Javed, M.; Smart, U.; Yaqub, T.; Hashmi, A.S.; Thammachoti, P. (2019). "Phylogenetic analysis of the Common Krait (Bungarus caeruleus) in Pakistan based on
Common_krait
Speakers of Austronesian languages
among Austronesian-speaking peoples that justifies their treatment as a "phylogenetic unit". This has led to the use of the term "Austronesian" in academic
Austronesian_peoples
Genus within Felidae
following relationships of living Panthera species: In 2018, results of a phylogenetic study on living and fossil cats were published. This study was based
Panthera
Species of bacterium
(rRNA), a genetic marker of bacterial evolution, is used in establishing phylogenetic relationships due to its highly conserved nature. 16S rRNA sequencing
Mycobacterium_lepromatosis
Type of aquatic ecosystem with flowing freshwater
American lotic insects: traits-based ecological applications in light of phylogenetic relationships". Journal of the North American Benthological Society.
River_ecosystem
Genus of plants
Tomotaro; Okazaki Keiichi; Arakawa Katsuro; Nagamine Tsukasa (2001). "Phylogenetic Analysis of Section Sinomartagon in Genus Lilium Using Sequences of the
Lilium
Language family indigenous to the South Caucasus
further study is required. A 2023 study employing Bayesian linguistic phylogenetics in conjunction with archaeological, ethnoecological, and human population
Kartvelian_languages
Genus of fishes
fishes of the family Acanthuridae (Perciformes: Teleostei)". Molecular Phylogenetics and Evolution. 26 (2): 190–201. Bibcode:2003MolPE..26..190C. doi:10
Paracanthurus
Family of venomous sea snails
old genus Conus. Using 329 species, the authors carried out molecular phylogenetic analyses. The results suggested that the authors should place all cone
Cone_snail
Short length polypeptides
to determine the validity of data obtained using this method. Ribosome profiling has been used to identify potential micropeptides in a growing number
Micropeptide
Species of large cat
Thapar 2004, p. 274. Barlow, A. C.; Ahmad, I. & Smith, J. L. (2013). "Profiling tigers (Panthera tigris) to formulate management responses to human-killing
Tiger
East Asian ethnic group
hmC-Seal, a method that covalently labels 5hmC for its detection and profiling. Other prominent Han Chinese who have made notable contributions the development
Han_Chinese
Family of hoofed mammals
morphology. They reverted from this classification in 2000. Molecular phylogenetic analyses since the latter half of the 2000s all show that hydropotes
Deer
1918–1920 global influenza pandemic
New York City in the same period. The study did find evidence through phylogenetic analyses that the virus likely had a North American origin, though it
Spanish_flu
Grouping of people
Slavic signal from modern-day Ukraine. Underhill, Peter A. (2015), "The phylogenetic and geographic structure of Y-chromosome haplogroup R1a", European Journal
Slavs
Ethnic group
; Ehret, C.; Assefa, S.; Mulligan, C. J. (29 April 2009). "Bayesian phylogenetic analysis of Semitic languages identified an Early Bronze Age origin of
Arabs
Life arising from non-living matter
between Bacteria and a clade formed by Archaea and Eukaryota in the phylogenetic tree of life. It lived over 4 Gya. A minority of studies have placed
Abiogenesis
Family of mammals
(2013) depicts the phylogeny of basal living and extinct groups. The phylogenetic relationships of living felids are shown in the following cladogram:
Felidae
Species of amphibian
(November 2004). "The History of a Nearctic Colonization: Molecular Phylogenetics and Biogeography of the Nearctic Toads (Bufo)". Evolution. 58 (11):
American_toad
Relationship between language and human evolution
its anatomical prerequisites extends, at least in principle, from the phylogenetic divergence of Homo from Pan to the emergence of full behavioral modernity
Origin_of_language
Extinct species of mammoth
mammoth (Proboscidea, Mammalia): New data and phylogenetic analyses of Elephantidae". Molecular Phylogenetics and Evolution. 26 (3): 421–434. Bibcode:2003MolPE
Woolly_mammoth
Realm of viruses
Dyall-Smith M, Jalasvuori M, Du S, Oksanen HM (March 2023). "ICTV Virus Taxonomy Profile: Sphaerolipoviridae 2023". J Gen Virol. 104 (3). doi:10.1099/jgv.0.001830
Singelaviria
Species of chestnut tree
closely related to the horse chestnut, which is in the family Sapindaceae. Phylogenetic analysis indicates a westward migration of extant Castanea species from
American_chestnut
Species of mammal in Asia
Mustelidae (weasels and relatives) and Mephitidae (skunks and relatives). Phylogenetic relationship of the red panda based on analysis of The family Ailuridae
Red_panda
Intense armed conflict
https://escholarship.org/uc/item/8jr9v920. Gómez, José María et al. (Summer 2016). "The phylogenetic roots of human lethal violence," Nature, vol. 538 (7624), https://www
War
Species of mammal
"Mitogenomic analysis of Rüppell's fox (Vulpes rueppellii) confirms phylogenetic placement within the Palaearctic clade shared with its sister species
Red_fox
Female sex organ in animals
a phenomenon that has not been found in any other eutherian mammal. Phylogenetic analyses have suggested that, like in lemuroids, this trait must have
Animal_clitoris
Species of Australian marsupial
species from the same family have been identified. The following is a phylogenetic tree based on mitochondrial genome sequences: Placement of the family
Numbat
Medium-sized toothed whale species
82 to 20.12 mya, and they are considered to be sister taxa. A later phylogenetic study conducted in 2020 suggested that the narwhal split from the beluga
Narwhal
Family of carnivoran mammals
other carnivorans is shown in the following phylogenetic tree, which is based on the molecular phylogenetic analysis of six genes in Flynn (2005) with
Bear
Herrera, Spindler & Bronzati (2026) redescribe the anatomy and study the phylogenetic affinities of Dakosaurus maximus on the basis of data from a new specimen
2026 in archosaur paleontology
2026_in_archosaur_paleontology
Cultivated fruit
1021/jf403644r. PMID 24328399. Xi, W.; Zheng, H.; Zhang, Q.; Li, W. (2016). "Profiling Taste and Aroma Compound Metabolism during Apricot Fruit Development and
Apricot
Use of empirical methods to study algorithms
performance profiling, resulting in a new algorithmic strategy conceived in light of the profiling along with other considerations. Profilers that collect
Empirical_algorithmics
Systematic error in phylogenetics
In phylogenetics, long branch attraction (LBA) is a form of systematic error whereby distantly related lineages are incorrectly inferred to be closely
Long_branch_attraction
Genus of snakes
the recognition of only three species of anaconda. The result of their phylogenetic analysis is represented below: In a response paper, Dubois et al. questioned
Anaconda
Free software package for phylogenetic analysis of rRNA
The ARB Project is a free software package for the phylogenetic analysis of rRNA and other biological sequences including DNA and protein sequence. It
ARB_Project
Province in South China
its accent, Cantonese can also be used, in a wider sense, for the phylogenetically related residents and Chinese dialects outside the provincial capital
Guangdong
Clade of reptiles
science, and new discoveries are regularly covered by the media. Under phylogenetic nomenclature, dinosaurs are usually defined as the group consisting of
Dinosaur
Organism that produces both male and female gametes
PMID 29207942. Erisman BE, Petersen CW, Hastings PA, Warner RR (October 2013). "Phylogenetic perspectives on the evolution of functional hermaphroditism in teleost
Hermaphrodite
Colombian footballer (born 1991)
enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa". Molecular Phylogenetics and Evolution. 100:
James_Rodríguez
One of the two categories of Indigenous Australians
Population and Housing, Aboriginal and Torres Strait Islander Peoples Profile, Table I01". Australian Bureau of Statistics. 2022. Retrieved 19 October
Aboriginal_Australians
Medium-sized wild cat
000 years ago following the Last Glacial Period. According to a 2006 phylogenetic study, the ancestor of five extant felid lineages—Lynx, Leopardus, Puma
Canada_lynx
Order of arachnids
which were marine animals. This 2019 cladogram illustrates the spiders' phylogenetic relationships. Arachnids lack some features of other chelicerates, including
Spider
PHYLOGENETIC PROFILING
PHYLOGENETIC PROFILING
PHYLOGENETIC PROFILING
PHYLOGENETIC PROFILING
PHYLOGENETIC PROFILING
PHYLOGENETIC PROFILING
PHYLOGENETIC PROFILING
PHYLOGENETIC PROFILING
PHYLOGENETIC PROFILING