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In genetics, haplotype estimation (also known as "phasing") refers to the process of statistical estimation of haplotypes from genotype data. The most
Haplotype_estimation
Group of genes from one parent
A haplotype (haploid genotype) is a group of alleles in an organism that are inherited together from a single parent. Many organisms contain genetic material
Haplotype
This is a list of notable software for haplotype estimation and genotype imputation. Alphabetical order: AlphaImpute Beagle cnF2freq DAGPHASE Eagle fastPHASE
List of haplotype estimation and genotype imputation software
List_of_haplotype_estimation_and_genotype_imputation_software
DNA-based genetic test
information on which variants are present. As a result, a step called haplotype estimation ("phasing") is required to guess which variants are inherited from
Genealogical_DNA_test
Professor of Statistical Genomics
group was responsible for the haplotype estimation and genotype imputation for the UK Biobank dataset. He co-leads the Haplotype Reference Consortium. He has
Jonathan_Marchini
Statistical inference of unobserved genotypes
hidden Markov model construct. List of haplotype estimation and genotype imputation software Haplotype estimation Scheet, Paul; Stephens, Matthew (2006)
Imputation_(genetics)
genetic linkage. Haplotype phasing (also called haplotype estimation) refers to the process of reconstructing individual haplotypes, important for determining
Linked-read_sequencing
following functionalities: LD & haplotype block analysis Haplotype population frequency estimation Single SNP and haplotype association tests Permutation
Haploview
Repetitive DNA sequence
containing N number of haplotypes. For example, if a haplotype has been observed twice in a database of N = 2000, the frequency of that haplotype will be: 2/2000
Y-STR
S2CID 205421216. Delaneau O, Howie B, Cox AJ, Zagury JF, Marchini J (2013). "Haplotype estimation using sequencing reads". Am J Hum Genet. 93 (4): 687–96. doi:10.1016/j
Mega2, the Manipulation Environment for Genetic Analysis
Mega2,_the_Manipulation_Environment_for_Genetic_Analysis
Inferred statistical population
manipulation allows exploration in the effects of missing populations on the estimation of population sizes and migration rates between two specific populations
Ghost_population
Measure of population differentiation
Frequencies, pg 294–295, S. Wright, Univ. of Chicago Press, Chicago, 1969 A haplotype map of the human genome, The International HapMap Consortium, Nature 2005
Fixation_index
Discrete probability distribution
Kamath, Govinda M.; Şaşoğlu, Eren; Tse, David (14–19 June 2015). Optimal haplotype assembly from high-throughput mate-pair reads. 2015 IEEE International
Poisson_distribution
Concept in genealogy and genetics
Browning, S. R. (2008). "Estimation of Pairwise Identity by Descent from Dense Genetic Marker Data in a Population Sample of Haplotypes". Genetics. 178 (4):
Identity_by_descent
Method of data analysis
A principal components analysis scatterplot of Y-STR haplotypes calculated from repeat-count values for 37 Y-chromosomal STR markers from 354 individuals
Principal_component_analysis
Dog breed
PMC 5492993. PMID 28445722. Refer Figure 4 and Supplementary Table S2: "Mean Haplotype Sharing Totals that Reach the 95% Significance Level between All Pairs
Irish_Wolfhound
Extinct subspecies of the gray wolf
worldwide revealed that one Kishu and one Siberian husky possessed the same haplotype as a Japanese wolf, indicating past cross-breeding. A more-refined study
Japanese_wolf
Biologist
2021-01-30. Excoffier, L.; Slatkin, M. (1995). "Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population". Molecular Biology and
Montgomery_Slatkin
How many different types are in a dataset
also be other categories, such as genera, families, functional types, or haplotypes. The entities of interest are usually individual organisms (e.g. plants
Diversity_index
factor for the number of gene lineages, zygosity mutations, and founding haplotypes present in today's Indigenous peoples of the Americas populations. The
Indigenous peoples of the Americas
Indigenous_peoples_of_the_Americas
Branch of phylogeny that analyzes genetic, hereditary molecular differences
referred to as its haplotype. In principle, since there are four base types, with 1000 base pairs, we could have 41000 distinct haplotypes. However, for organisms
Molecular_phylogenetics
Species of fish
; Tang, P.-C.; Chiu, T.-S. (2009). "Microsatellite and mitochondrial haplotype differentiation in blue mackerel (Scomber australasicus) from the western
Blue_mackerel
American geneticist (born 1965)
evolution, leading her to write her thesis on the "Patterns of nuclear haplotype frequency variation and linkage disequilibrium in a global sample of human
Sarah_Tishkoff
Group of related bird species in the Galápagos Islands
finches. In 2015–2016 studies, genome sequencing revealed a 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting
Darwin's_finches
Species of tortoise
C.; Ballasina, Donato L.P.; Zorgdrager, Fokla (2005). "Mitochondrial haplotype diversity in the tortoise species Testudo graeca from North Africa and
Hermann's_tortoise
Statistical phenomenon
reflects a normal statistical distribution. If two parents share the same haplotype and have one dominant allele and one recessive allele for each gene then
Regression_toward_the_mean
Species of large cat
Society. 100 (2 & 3): 169–189. Karanth, K. U. & Nichols, J. D. (1998). "Estimation of tiger densities in India using photographic captures and recaptures"
Tiger
Archaeological site in Tunisia
Leïla Ladjimi; Zalloua, Pierre A. (2016-05-25). "A European Mitochondrial Haplotype Identified in Ancient Phoenician Remains from Carthage, North Africa"
Carthage
Turkic nomadic people
indicated a partly European ancestry was that of the chieftain, whose haplotype is most frequently found in the Balkans." The study concluded that the
Cumans
families in testing. QTDT has also been extended to haplotype-based association mapping. Haplotypes refer to combinations of marker alleles which are located
Family-based_QTL_mapping
Matrilineal most recent common ancestor of all living humans
markers which give a mitochondrial "DNA signature" or "haplotype" (e.g. the CRS is a haplotype). Each marker is a DNA base-pair that has resulted from
Mitochondrial_Eve
The ancestral sickle cell haplotype to modern haplotypes (e.g., Cameroon/Central African Republic and Benin/Senegal haplotypes) may have first arose in
Genetic_history_of_Africa
Tiger population on the Indian subcontinent
revealed that the tigers in question had a Bengal tiger mitochondrial haplotype indicating that their mother was a Bengal tiger. Skin, hair and blood
Bengal_tiger
Polygenic phenotypic characteristic
G.; Sturm, Richard A. (2007). "A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation". Am. J. Hum
Eye_color
Branching diagram of evolutionary relationships between organisms
as Phylotree, feature internal nodes labeled with inferred ancestral haplotypes. The number of possible trees for a given number of leaf nodes depends
Phylogenetic_tree
M, et al. (December 2005). "Genome sequence, comparative analysis and haplotype structure of the domestic dog". Nature. 438 (7069): 803–19. Bibcode:2005Natur
List of organisms by chromosome count
List_of_organisms_by_chromosome_count
South Slavic ethnic group
2012. Mršić, Gordan; et al. (2012). "Croatian national reference Y-STR haplotype database". Molecular Biology Reports. 39 (7): 7727–41. doi:10.1007/s11033-012-1610-3
Croats
Genetic diversity in human populations
Moore JM, Roy J, Blumenstiel B, et al. (June 2002). "The structure of haplotype blocks in the human genome". Science. 296 (5576): 2225–9. Bibcode:2002Sci
Human_genetic_variation
Disease caused by the bacteria Salmonella Typhi
widespread globally. Global phylogeographical analysis showed dominance of a haplotype 58 (H58), which probably originated in India during the late 1980s and
Typhoid_fever
Breed of horse
When an estimation was made using microsatellite loci, the Newfoundland was found to have high autosomal diversity and a high number of haplotypes, some
Newfoundland_pony
Human Y-chromosome DNA haplogroup
Agnar Helgason first discovered the haplotype that was much later to become known as Q-L804. In 2000 the strange haplotype was called "branch-A" (i.e. R1b-branch
Haplogroup_Q-L804_(Y-DNA)
Ethnic group(s)
Zeferino; Olivares, Norma; Rivas, Fernando (September 2011). "Renin gene haplotype diversity and linkage disequilibrium in two Mexican and one German population
White_Mexicans
Forensic application of the study of biology
share a haplotype. A haplotype "is a group of alleles in an organism that are inherited together from a single parent". Sharing this haplotype among family
Forensic_biology
[page needed] However this claim is disputed by modern genetic studies on haplotype findings of Y-chromosomal ancestry amongst various Muslim communities
Islam_in_India
Human Y-chromosome DNA haplogroup
et al. (2017) report a M183-SM001 pattern of decreasing microsatellite haplotype variation (implying greater lineage age in the former areas) from the
Haplogroup_E-M35
Species of shark
estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves". PeerJ Computer Science. 6 e243. doi:10.7717/peerj-cs
Scalloped_hammerhead
Ethnic group
"High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews". Human Genetics
Arabs
Grouping by physical or social qualities
decreasing pattern from the equator north and south; frequencies for the haplotype for beta-S hemoglobin, on the other hand, radiate out of specific geographical
Race_(human_categorization)
associated TYR Arg402Gln (rs1126809), OCA2 Arg305Trp (rs1800401) and a 2-SNP haplotype in ASIP (rs4911414 and rs1015362) to skin type variation within a "fair/medium/olive"
Human_skin_color
Iranian ethnic group
predominance of haplogroup R1a1a*-M198 (>50%) and the sharing of the same modal haplotype...Although Greeks and Jews have been proposed as ancestors to Pathans
Pashtuns
Ethnic group indigenous to North Africa
DNA analysis of these specimens indicates that they carried paternal haplotypes related to the E1b1b1b1a (E-M81) subclade and the maternal haplogroups
Berbers
Recessive genetic disorder causing deafblindness
French-Acadian populations (Louisiana). Among Acadians, research into haplotype data is consistent with one single mutation being responsible for all
Usher_syndrome
Stratification of a genetic population based on allele frequencies
leave a genetic imprint on populations. Admixed populations will have haplotype chunks from their ancestral groups, which gradually shrink over time because
Population structure (genetics)
Population_structure_(genetics)
People of Lebanon
Institute of Anthropology in Paris, France, confirmed similarities in the Y-haplotype frequencies in Lebanese, Palestinian, and Sephardic Jewish men, identifying
Lebanese_people
DNA analysis of Filipino populations
studies done by Applied Biosystems and FamilyTreeDNA, wherein the R1b Y-DNA Haplotype common in Spain and Western Europe was detected among 12-13% of the sample
Genetic and anthropology studies on Filipinos
Genetic_and_anthropology_studies_on_Filipinos
Archaological dating based on mutation rate
depending on the available data and the method used for estimation. The two main methods of estimation, phylogeny-based methods and pedigree-based methods
Human mitochondrial molecular clock
Human_mitochondrial_molecular_clock
Ability to digest milk after infancy
selection is similar to that estimated for the resistance to malaria. Haplotype inferences were performed on data from Central Asia populations; selection
Lactase_persistence
through the incorporation of population-wide haplotype frequencies in the prior. The use of haplotypes to improve variant detection accuracy has been
SNV_calling_from_NGS_data
Mexicans of European and Amerindian ancestry
Zeferino; Olivares, Norma; Rivas, Fernando (16 December 2010). "Renin gene haplotype diversity and linkage disequilibrium in two Mexican and one German population
Mestizos_in_Mexico
Region of North Africa; western half of the Arab world
S; Torre, C (2008). "Analysis of Y-chromosomal SNP haplogroups and STR haplotypes in an Algerian population sample". International Journal of Legal Medicine
Maghreb
Species of single-celled organism
Clonal lineages of A1 include: CN-1CN-1, -2, -4, -5, -6, -7, -8 – mtDNA haplotype Ia, China in 1996–97 CN-3 – Ia, China, 1996–97 CN-10 – Ia, China, 2004
Phytophthora_infestans
American geneticist
genetic evaluations of crossbred animals, methodology related to the estimation of genetic parameters and the prediction of genetic merit in populations
Rohan_Fernando_(geneticist)
Chen W, et al. (February 2007). "A Three–Single-Nucleotide Polymorphism Haplotype in Intron 1 of OCA2 Explains Most Human Eye-Color Variation". American
Sexual dimorphism in human physiology
Sexual_dimorphism_in_human_physiology
Wolf subspecies
indica) is formed by two closely related female lineage mitochondrial DNA haplotypes that fall within the Canis lupus pallipes subspecies of the gray wolf
Indian_wolf
Americans of Chinese ancestry
distributions in European-American and Han Chinese populations. Besides, rarer haplotype is found to be absent in the samples of Han Chinese, and they also possess
Chinese_Americans
Tiger subspecies endemic to Sumatra
diagnostic mitochondrial DNA nucleotide sites, ten mitochondrial DNA haplotypes and 11 out of 108 unique microsatellite alleles. The relatively high genetic
Sumatran_tiger
Abnormal collection of air in the pleural space
syndrome are absent. In addition to the genetic associations, the HLA haplotype A2B40 is also a genetic predisposition to PSP. A traumatic pneumothorax
Pneumothorax
Chinese biotechnology company
(2016-12-01). "The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes". GigaScience. 5 (1): 42. doi:10.1186/s13742-016-0148-z
Complete_Genomics
Mesolithic hunter-gatherers of Iranian Plateau
Iran_HotuIIIb ancestry. IBD analysis then shows that Khvalynsk I0434 shares long haplotype blocks with Nalchik man, consistent with recent gene flow from a Nalchik/Unakozovo-like
Iranian_hunter-gatherers
Subject in population genetics
Japanese cluster is said to be the most similar with the Korean one; in a haplotype-based study, the Japanese cluster was found to share 87–94% of its genetic
Genetic and anthropometric studies on Japanese people
Genetic_and_anthropometric_studies_on_Japanese_people
Extinct genus of bears
during the Last Glacial Maximum, with four distinct lineages across five haplotypes intermingled with eastern Beringian specimens. The last common ancestor
Arctodus
Sex chromosome in the XY sex-determination system
M, et al. (December 2005). "Genome sequence, comparative analysis and haplotype structure of the domestic dog". Nature. 438 (7069): 803–819. Bibcode:2005Natur
Y_chromosome
Time elapsed since an allele first appeared
ancestor (TMRCA) between hundreds or thousands of chromosomal sequence (haplotype) pairs. This information is then combined using a composite likelihood
Allele_age
Invasive ant species
Based on mitochondrial DNA, examined haplotypes do not form a monophyletic clade. Some of the examined haplotypes form a closer relationship to S. megergates
Red_imported_fire_ant
Representative Wolf and Domestic Dog Haplotypes". Zoological Science. 26 (11): 765–70 Morita M., Yagi H., 2015, Size estimation of so-called "Chichibu wild dog"
Timeline of extinctions in the 20th century
Timeline_of_extinctions_in_the_20th_century
Species of fish
Germany, Ukraine, Italy, and the Neretva basin in Bosnia and Herzegovina. Haplotype data indicates that European ginbuna derive from populations in either
Ginbuna
Lab technique in cellular biology
variants is allele-specific expression (ASE): the variants from only one haplotype might be preferentially expressed due to regulatory effects including
RNA-Seq
People of Mexico
S2CID 41443294. Valdez-Velazquez, Laura L.; et al. (16 December 2010). "Renin gene haplotype diversity and linkage disequilibrium in two Mexican and one German population
Mexicans
"Demographic history differences between Hispanics and Brazilians imprint haplotype features". G3. 12 (5): e0152573. doi:10.1093/g3journal/jkac111. PMC 9258545
Race_and_ethnicity_in_Brazil
includes transcript-level RNA-Seq quantification, allele-specific and haplotype analysis and can estimate transcript abundances of the multiple isoforms
List of RNA-Seq bioinformatics tools
List_of_RNA-Seq_bioinformatics_tools
mean found their European admixture to be 82 percent. On average, 68 haplotypes account for 95% of the chromosomes in Mexicans. According to a nationwide
Ethnic groups in Latin America
Ethnic_groups_in_Latin_America
American geneticist
phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation". Genetics. 132 (2): 619–633
Keith_A._Crandall
Japanese prehistorical period
combined discrimination of modern/Ancient genome-wide shared alleles and haplotypes: Differentiated demographic history reconstruction of Tai-Kadai and Sinitic
Jōmon_period
Species of orthopteran insect
lineages from mtDNA haplotypes, where each occupied a discrete geographic region. The average genetic difference between haplotypes was 4.8%. This genetic
Deinacrida_connectens
Neolithic–Eneolithic archaeological culture of southeastern Europe
Beaker culture groups, which displayed similar frequencies of H-bearing haplotypes. A study by Mathiesson et al., published 2018 in Nature, included a whole-genome
Cucuteni–Trypillia_culture
Filipinos and it is discovered that about 0.95% of the samples have the Y-DNA Haplotype "H1a", which is most common in South Asia and had spread to the Philippines
Ethnic groups in the Philippines
Ethnic_groups_in_the_Philippines
Finnic ethnic group
oldest permanent inhabitants. On the other hand, some recent linguistic estimations suggest that Finno-Ugric speakers arrived around the Baltic Sea considerably
Estonians
carry uniparental haplotypes primarily found today in Western Europe, the individuals buried in the Muslim cemetery carry haplotypes associated with North
Genetic_history_of_Italy
People of the Canary Islands
Hernandez A, Sanchez JJ, Cuellas JA (March 2005). "Y-chromosome STR haplotypes in the Canary Islands population (Spain)". Forensic Science International
Canary_Islanders
Y chromosome haplogroup
access databases featuring I-M253, including: [1] Archived 2011-01-04 at the Wayback Machine YHRD : Y-Chromosome STR Haplotype Reference Database I1 YTree
Haplogroup_I-M253
Family of parasitic flatworms
structure of Clinostomum complanatum (Trematoda: Digenea) with new data on haplotype diversity of flukes from Slovakia and Italy". Parasite. 32: 3. doi:10
Clinostomum
9th and 10th century Magyar campaign
connection ... The single X2f maternal haplotype of the chief (sample 11) is of particular interest, as this haplotype is most probably of south Caucasian
Hungarian conquest of the Carpathian Basin
Hungarian_conquest_of_the_Carpathian_Basin
Genome assembly algorithm
Afterwards, it produces consensus contigs construction and performs haplotype assembly. A study compared several genome assemblers on single cell E
SPAdes_(software)
Ethnic group
inside and outside of the Carpathian range) in terms of mitochondrial haplotype variability. The population within the Carpathian range was found to have
Romanians
People of Tunisia
El-Gaaied, Amel; Hmida, Slama (2015). "HLA Class I and Class II Alleles and Haplotypes Confirm the Berber Origin of the Present Day Tunisian Population". PLOS
Tunisians
Human Y chromosome DNA grouping indicating common ancestry
Shabwah and Al Bayda were also confirmed to belong to the basal D0/D2 haplotype. A 2021 study by Mengge Wang et al. found one sample of Y-chromosome DE-M145
Haplogroup_DE
haplotypes of the MUC19 gene in modern humans as inherited from Neanderthals who in turn likely inherited it from Denisovans, and find this haplotype
2025_in_paleomammalogy
Method of archaeological study
061014798. PMC 31832. PMID 11296282. Baker LE (2001). Mitochondrial DNA haplotype and sequence analysis of historic Choctaw and Menominee hair shaft samples
Ancient_DNA
American computational biologist and researcher
Whole-Genome Resequencing" in Genes, Genomes, Genetics, 2013 "Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding
Amanda_M._Hulse-Kemp
HLA-NET explicitly requests that frequency estimates, for alleles or haplotypes, be validated by checking their conformity with Hardy–Weinberg expectations
HLA-NET
HAPLOTYPE ESTIMATION
HAPLOTYPE ESTIMATION
Girl/Female
Biblical
Estimation, thought.
Biblical
estimation; thought
Biblical
the estimation of the Lord
Boy/Male
Biblical
The estimation of the Lord.
HAPLOTYPE ESTIMATION
HAPLOTYPE ESTIMATION
Surname or Lastname
English (of Norman origin)
English (of Norman origin) : from Old French bel(e) ‘fair’, ‘lovely’ (see Beau), either a nickname for a handsome man or a metronymic from this word used as a female personal name.English : habitational name from places so named in Northumberland and West Yorkshire. The former of these (Behil in early records) comes from Old English bēo ‘bee’ + hyll ‘hill’; the latter (Begale in Domesday Book) is from Old English bēag ‘ring’, here probably used in the sense ‘river bend’, or an unattested personal name Bēaga derived from this word + halh ‘nook’, ‘recess’.French (Béal) : topographic name for someone who lived by a mill race, from the Lyonnaise dialect term béal, bezale, bedale (of Gaulish origin).Americanized spelling of German Biehl or Bühl (see Buehl).Lt. Col. Thomas Beal(e) (c.1621–c.1676) of London settled in York Co., VA, about 1650.
Boy/Male
English
A surname meaning swarthy, used occasionally as a first name. Famous bearer, 18th-century actor...
Surname or Lastname
English
English : possibly a habitational name from Mill Ham, Devon, or Millham Farm in Cornwall and Hereford, or perhaps a variant of Mileham.
Surname or Lastname
Scottish
Scottish : Anglicized form of Gaelic Mac Iain, patronymic from Iain, one of the Gaelic forms of John. This name is found in many other spellings, including McCain, Kean, and McKean. In some cases it may also be a variant of Coyne.English : variant spelling of Cane.English (of Norman origin) : habitational name from Caen in Calvados, France, named with the Gaulish elements catu ‘battle’ + magos ‘field’, ‘plain’.French (Caïn) : from the Biblical name Cain (Hebrew Qayin), probably applied as a derogatory nickname for someone who was considered to be treacherous.Spanish (CaÃn) : habitational name from a place called CaÃn in León.
Girl/Female
Muslim
Heaven. Garden.
Boy/Male
Arabic, Muslim
Glittering; Shining
Girl/Female
Muslim/Islamic
A pious woman daughter of Amr al-Basriyah was so named
Girl/Female
Tamil
Witness
Girl/Female
Indian, Telugu
Less Energetic and Calm
Boy/Male
Latin American
Of Laurentum. From the place of the laurel leaves. Can also be interpreted as the English...
HAPLOTYPE ESTIMATION
HAPLOTYPE ESTIMATION
HAPLOTYPE ESTIMATION
HAPLOTYPE ESTIMATION
HAPLOTYPE ESTIMATION
v. t.
To rate highly; to have in high esteem; to hold in respect and estimation; to appreciate; to prize; as, to value one for his works or his virtues.
n.
A species of divination by meteors, chiefly by thunder and lightning, which was held in high estimation by the Romans.
n.
A method of taking photographic pictures, on paper sensitized with iodide of silver; -- also called Talbotype, from the inventor, Mr. Fox. Talbot.
v. t.
An opinion or judgment of the worth, extent, or quantity of anything, formed without using precise data; valuation; as, estimations of distance, magnitude, amount, or moral qualities.
n.
A photographic picture copied from the negative on glass; a photographic transparency.
v. t.
To esteem lightly; to treat as of little worth; to hold in mean estimation; to despise.
n.
The act of valuing, or of estimating value or worth; the act of setting a price; estimation; appraisement; as, a valuation of lands for the purpose of taxation.
superl.
Exalted in social standing or general estimation, or in rank, reputation, office, and the like; dignified; as, she was welcomed in the highest circles.
v. t.
To raise to estimation; to cause to have value, either real or apparent; to enhance in value.
a.
Invaluable; being beyond estimation.
n.
The estimation of temperature by the use of a thermometric apparatus.
n.
The act of estimating one's self; self-esteem.
n.
The estimation of the specific gravity of urine by the urinometer.
n.
A picture taken on "milky" glass.
n.
The cause or reason of shame; that which brings reproach, and degrades a person in the estimation of others; disgrace.
n.
Favorable estimation; hence, consideration; reputation; fame; public sentiment or esteem.
n.
Esteem due or paid to worth; high estimation; respect; consideration; reverence; veneration; manifestation of respect or reverence.
n.
Same as Calotype.
n.
Rank; grade; station; estimation.
n.
The judgment or sentiment which the mind forms of persons or things; estimation.