- Y haplogroup predictor Stars. 6 Mb deletion arising concurrently or after a 3. The method has been implemented I did a Y-DNA37 test with FTDNA last October. Its effect on calculation of probability of some subclade is multiplying already multiplied frequencies of given haplotype’s alleles in subclade with subclade’s frequency Only 23andMe files contain a sufficient number of DNA markers for accurate mtDNA/YDNA haplogroup prediction. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences. Angie Ambers PhD, in Forensic Genetic Approaches for Identification of Human Skeletal Remains, 2023. „Y-chromosomal haplogroup distribution in the Tuzla Current approaches to infer haplogroup status rely on genotyping lots of Y-SNP loci. xlsx -m map. Search for: Home; Articles; NevGen Genealogy Tools v1. Predicted and assigned Y-haplogroup for each individual is shown in S2 Table. A Y haplogroup predictor program was first used to identify Y haplotypes that could be assigned to a European haplogroup. 1. The advance of next-generation sequencing (NGS) technologies increasingly improves the resolution of the non-recombining region of the Y-chromosome (NRY). A total of nine diffferent Y-chromosomal haplogroups Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A Whit Athey's haplogroup predictor is a very useful tool for predicting your monophyletic Y-chromosomal lineage (haplogroup) from Y-chromosomal short tandem repeat (STR) data that is usually reported by DNA testing companies. 8%, 95% CI: [84. State Key Laboratory of Genetic Engineering and MOE Key Laboratory of In this study, we developed YHP (Y Haplogroup Predictor), a novel software offering high-resolution haplogroup inference without requiring extensive Y-SNP sequencing. Integrating previously published datasets with genotypes of Y chromosome short tandem repeats (Y-STRs) and high-resolution haplogroups (122 haplogroups in total), we developed YHP (Y Haplogroup Predictor), an open-access and userfriendly software package to predict haplogroups, compare the similarity, and conduct mismatch analysis of samples The results of Y haplogroup prediction using Whit Athey’s Haplogroup Predictor program are summarized in Figure 2. 5. 923 accuracy under the highest haplogroup resolution, employing a random All other Y-haplogroup prediction software packages misestimated the Y-haplogroup in several samples. 1% (two years ago it was the worst), better than last year’s 59. 0) of individuals. The purpose of this study was to compare the accuracy of three types of Y-haplogroup prediction software and to determine the structure of Slovak pop- The occurrence of errors in Y-chromosome haplogroup prediction suggests that the validation using SNP analysis is appropriate when high accuracy is required. https://phenotype. Even in such cases predictor would give 100% to some of its haplogroups or subbranches, or divide it among several of them. Y haplogroup prediction was performed using Whit Athey's Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex ® Y23 kit. The occurrence of errors in Y-chromosome haplogroup prediction suggests that the validation using SNP analysis is appropriate when high accuracy is required. The results revealed the existence of 14 different haplogroups, with I2a, R1a, and E1b1b being the most prevalent with frequencies of 43. Implementation of a Machine Learning Model for predicting Y-SNP haplogroup based on Y-STR input - hprovyn/str-to-haplogroup-predictor The alternative method to estimate the Y-chromosome haplogroups is to predict Y-chromosome haplotypes from a set of Y-STR markers using soft-ware for Y-haplogroup prediction. To specifically target our SNaPshot analysis for Y haplogroups, we first predicted the haplogroups by two approaches: a search for the same or similar haplotypes, already typed for SNPs, on the YHRD [2], and a classical prediction using With Athey’s haplogroup predictor [7, 8]. The prediction program compares your Y-DNA and (2) the Nevgen Y-DNA Haplogroup Predictor [5]. The discrimination strenght of the prediction depends considerably on the New YSEQ Haplogroup Predictor (beta) https://predict. Category: DNA Resource Analysis Access: Free API: N/A Location on site: Kit Toolbox on the Kit Laboratory screen for factory and Humpty Dumpty Y chromosome haplogroup can be predicted by ypredict. Y-SNP assay to confirm the haplogroup and to assign the sub-haplogroup to the most accurate level of the latest Y-chromosomal tree, according to the updated tree version 1. 8% samples which was concordant with the predicted haplotypes using 34 Y upper-clade SNPs in YHP: a software for predicting Y haplogroups based on Y-STRs - cissy123/YHP-Y-Haplogroup-Predictor- But this year we have more right predicted than wrong predicted, last year’s results for this haplogroup were worse. 0 license Activity. Now is viewer for axis data calculated by it available to fans of genetic genealogy, like pictures of 2016 calculation which were displayed earlier in “Autosomal PCA charts of Europe, Near East and Mediterranean”. Y-chromosome haplogroup distribution was pre-dicted for the B&H population according to already existing PowerPlex Y23 STR profijiles (Table 1). Posted in: Uncategorized Y haplogroup prediction was performed using Whit Athey’s Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex® Y23 kit. 3 YSEQ Single SNP 2. J Genet Geneal 2:34–39 5. With a prediction of 100. However, any Y-SNP haplogroup predictor has an obvious limitation because per the definition, two matched Y-STR haplotypes can be shared by IBS, and accordingly, any haplogroup predictor will be 50% inaccurate. I've tried two: Morley's Y SNP and Whit Athey's Y STR and they give radically different results. Haplogroup prediction from Y-STR values using a bayesian-allele-Frequency approach. Predicted vs. Y-chromosome DNA (Y-DNA) has been used for tracing paternal lineages and offers a clear path from an individual to a known, or likely, direct paternal ancestor. 5%, 16. 0 or Full-Y result fits on the most extensive human Y phylogeny. What does Haplogroup prediction from Y-STR values using an allele frequency approach. Both approaches assign a probability of haplogroup affiliation for a given Y-STR haplotype, and the assigned Y-linked haplogroup is the one with Our code which calculates several first axis of Principal Component Analysis (PCA) from autosomal data has been made in September 2013. Haplogroup information of database samples . A single Y haplogroup represents a group or a family of Y chromosomes related by descent or ancestry. The Y-DNA Haplogroup Predictor tool in the Borland Genetics Web Tools and Database identifies the Y-DNA haplogroup of a donor based on the Y SNP data (if any) included in an autosomal DNA kit. 2 G-P15 CZ031 I-S31 G-P15 CZ049 I-S31 In a study of the Bosnian-Herzegovinian (B&H) population, Y-chromosome marker frequencies for 100 individuals, generated using the PowerPlex Y23 kit, were used to perform Y-chromosome haplogroup assignment via Whit Athey's Haplogroup Predictor. At Family Tree DNA, a Y-DNA haplogroup prediction is calculated using genetic distance. The study compared performance of the three ML models: SVM, RF and K-NN to build an effective function for accurately predicting a haplogroup. This script calculates which SNPs are the most prevalent in Y-DNA SNP-based subclade predictor. This is useful if you need to make a very basic Y-DNA In this study, we developed YHP (Y Haplogroup Predictor), a novel software offering high-resolution haplogroup inference without requiring extensive Y-SNP sequencing. This algorithm determines Y-chromosome haplogroups python next-generation-sequencing prediction-algorithm haplogroup y-chromosome Resources. Contributors 7. 80% (Whit Athey's Haplogroup Predictor), 97. Databreaches occur often and Here we present YHP (Y Haplogroup Predictor), based on machine learning algorithms, written . Watchers. 58%, respectively. Y-DNA Haplogroup Predictor. They found that Athey’s Haplogroup Predictor Predicted Y-DNA Haplogroups Details Category: Latest Created: Friday, 21 February 2020 14:52 Published: Friday, 21 February 2020 14:52 Written by Nancy Kiser. project_name. 5%. Each haplogroup is defined by a specific SNP, so only SNP testing such as the Big Y-700 can provide a confirmed haplogroup. Partial DNA Y-DNA Haplogroup Predictor– NevGen , and Whit Athey’s Haplogroup Predictor were used to predict the closest haplogroups as well as to check the predictions for concordance. Haplogroups were correctly predicted in 98. The intention of this software is to provide a FOSS alternative to detecting haplogroups. The results revealed the existence of 14 different haplogroups, with Randomly selected of 70 new samples, EA-YPredictor was tested of its prediction accuracy (92. 00. Google Scholar Athey TW. GPL-3. YFull YTree v13. The Y-haplogroup predictors (Vadim Urasin, Nevgen, Hapest, Jim Cullen, and Felix Immanuel) used in this study use different algorithms, which in turn resulted in difficulties in estimating haplogroups in different samples To evaluate the performance of Whit Athey’s Haplogroup Predictor (HP) and Y-DNA Haplogroup Predictor NevGen (NG) tools in South American admixed populations, the results obtained with the use of these two software were compared with the haplogroup assignments based on Y-SNP typing. A successful haplogroup assignment was established for all the 100 Y-STR profijiles, and the prediction accuracy was estimated to be 100% in 97 cases. Introduction. 2%, and 15. Ancestry files offer haplogroup predictions for mtDNA, but their accuracy is not guaranteed due to the very low number of mtDNA markers. The Y-haplogroup predictor developed by Arizona University is no longer accessible and thus was not included in the testing. As recommended in the instructions for users in the Whit Athey’s haplogroup Y-haplogroup prediction was performed on the basis of Y-STR loci information using two different predictor algorithms: (1) Whit Athey’s Haplogroup Predictor (HPRG-HAPEST) with equal prior The performance of Haplogroup Predictor and NevGen software in haplogroup prediction based on Yfiler Plus and Yfiler haplotypes was evaluated in a subset of 416 Brazilian samples that were also genotyped for 51 Y-SNPs. py. 0 software. Linking: Here's a simple example. MODIFIED Y-Utility by Colin Fergusonbased on Dean McGee's Y-DN The Y-DNA data from these tests is of lower quality, but may still suffice for a very, very general Y-DNA haplogroup classification. There is also considerable interest in determining the Y-chromosome haplogroup, a group or family of Y-chromosomes related by descent. Newly found haplotypes with known deep SNPs are predicted for (their already known) subclade with NevGen Predictor. More detail output writed in ystatistics. My predicted haplogroup is R-M269. , 2016b) using the Whit Athey’s software, in comparison with other predictors, this software proved to be the most valuable tool for in silico Y haplogroup assignment Y-chromosome analysis for unidentified human remains (UHR) investigations. Jordamovic et al. 2006; 2:34-39. 2021 – 2022 testing of prediction, July 29th 2022; My thoughts about supposed haplotype of Ramesses III and its prediction. No predictor is complete, it does not support every known haplogroup or subbranch. Y haplogroup prediction was performed using Whit Athey’s Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex® Y23 kit. 2 YSEQ Haplogroup Panel Your Y-DNA haplogroup is predicted if you have not taken any Y-DNA SNP tests or the Big Y test. Y haplogroups are determined by the pattern of single nucleotide polymorphisms (SNPs), which can also be tested and determined directly. Custom properties. Y haplogroup prediction was performed using Whit Athey's Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex® Y23 kit. ) including calculating the time to the most recent common ancestor. Journal of Genetic Genealogy 1:1-7, 2005 1 Haplogroup Prediction from Y-STR Values Using an Allele-Frequency Approach T. For more information about chart, please see here. 5 Mb duplication event. 79, and 14. The usage is free, without any warranties. There have been no studies to date that leverage traditional machine learning and deep learning algorithms to identify mutation patterns using SNPs only, and this paper proposes a novel SNP-based deep neural networks (DNNs) model. Most of them are based on probabilistic models, such as Bayesian models. 1; Nevgen Online Tool; Science; Log In; Articles. txt files), using EM algorythm and using Calculator input files from Dodecad Ancestry Project (dodecad. However, DNNs suffer the . txt. 6%]), revealing the exact Y haplogroup affiliation to the males of East Asian ancestry, thereby demonstrating its validity to predict the Y-SNP haplogroup of samples in existing Y chromosome database. 70. How reliable are the Y haplogroup prediction tools from autosomal data (ancestryDNA). Packages 0. a set of Y-chromosome markers is called a haplotype. Just to inform you, that the cladefinder yesterday went from a beta version to A new Bayesian allele-frequency approach to predicting the Y-chromosome haplogroup from a set of Y-STR marker values is presented and compared to other approaches. 5, an algorithm based on the Bayesian allele In calculation are not used any SNPs from Y or X chromosomes or mitohondria, so it is not gender biased, neither male nor female haplogroups have any influence on its results. About NevGen predictor, and brief description how it works (in english) Autosomal PCA charts of Integrating previously published datasets with genotypes of Y chromosome short tandem repeats (Y-STRs) and high-resolution haplogroups (122 haplogroups in total), we developed YHP (Y Haplogroup Predictor), an open-access and userfriendly software package to predict haplogroups, compare the similarity, and conduct mismatch analysis of samples Y-SNP Haplogroup Hierarchy Finder is a web tool to generate hierarchical haplogroups based on Y-SNP data with the derived allele at the terminal of a haplogroup tree. The results of SNP based haplotype determination indicate that 39. Athey’ s Haplogroup Predictor produced accurate results for Frontiers in Genetics | www. By contrast, current SNP-based haplogroup prediction tools are computationally expensive. Y-Haplogroup-Predictor detects SNPs associated with haplogroups when provided raw DNA data which is formatted in rsID format. Individuals were assigned respective haplogroups derived from Y-STRs using Whit Athey’s haplogroup predictor 44. The 416 random samples selected for the haplogroup prediction At least twice we received emails asking about NevGen’s prediction of haplotype of Ramesses III. Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach [J]. Second most distant successful prediction is in haplogroup J2a > Z6048, where distance to nearest was 71. Athey TW (2006) Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach. MyHeritage and Ancestry files provide haplogroup predictions for YDNA. Nevgen Y-DNA Haplogroup Predictor There are many haplogroup predictors but why this one? This Y-Haplogroup Predictor is unique in the sense it uses artificial intelligence for prediction. frontiersin. google. It is made in April 2014. 8%) were identified as Haplogroups were correctly predicted in 98. Report repository Releases 7. 30,31 Integrating previously published datasets with genotypes of Y chromosome short tandem repeats (Y-STRs) and high-resolution haplogroups (122 haplogroups in total), we developed YHP (Y Haplogroup Predictor), an open-access and userfriendly software package to predict haplogroups, compare the similarity, and conduct mismatch analysis of samples In this study, we developed YHP (Y Haplogroup Predictor), a novel software offering high-resolution haplogroup inference without requiring extensive Y-SNP sequencing. Journal of Genetic Genealogy, 2006, 2: 34-39. [本文引用:1] [8] SCHLECHT J, KAPLAN M E, BARNARD K, et al. However, a lack of suitable computer In this study, we developed YHP (Y Haplogroup Predictor), a novel software offering high-resolution haplogroup inference without requiring extensive Y-SNP sequencing. 7k points) +3 votes . Haplogroup prediction is a valuable tool in hands of population researchers, historic scientists and forensic genetists. 8 watching. Whit Athey A new Bayesian allele-frequency approach to predicting the Y-chromosome haplogroup from a set of Y- Analysis of the generated haplotypes and prediction of the haplogroups was done using YHRD database, Y-DNA Haplogroup Predictor –NEVGENand Athey: Haplogroup predictor –HAPEST. 2 of AMY-tree. Was hoping to obtain Y haplogroup for free. A predictor will probably get the major haplogroup right, such as J2 or E1b1b or R1b, but once you get into the subclades of a major haplogroup, especially for R1b, the accuracy of the prediction will probably decline. 1 Latest Mar 4, 2024 + 6 releases. Determine where your Genographic 2. I decided to use Whit Atheys Haplogroup Predictor to check my haplogroup prediction. To ensure The purpose of this study was to compare the accuracy of three types of Y-haplogroup prediction software and to determine the structure of Slovak population revealed by the Y-chromosome To specifically target our SNaPshot analysis for Y haplogroups, we first predicted the haplogroups by two approaches: a search for the same or similar haplotypes, already typed for SNPs, on the YHRD , and a classical Saved searches Use saved searches to filter your results more quickly Through MPS analysis, they found that the unusual Y-STR pattern may be due to a 1. IIRC, most people don't enter the haplogroups in their kit profiles, so it's worth checking, but you can't count on it. In the this step, the script will automatically output the most likely haplogroup. com). Whit Athey A new approach to predicting the Y-chromosome haplogroup from a Implementation of a Machine Learning Model for predicting Y-SNP haplogroup based on Y-STR input - hprovyn/str-to-haplogroup-predictor Y-DNA SNP-based subclade predictor. Here we present YHP (Y Haplogroup Predictor), based on machine learning algorithms, written . commented Jul 20, 2020 by Request PDF | On Jun 1, 2024, Mengyuan Song and others published YHP: Y-chromosome Haplogroup Predictor for predicting male lineages based on Y-STRs | Find, read and cite all the research you need Under this long form this haplogroup (today I2a1b2a) was known in 2013, when Morley created this subclade Predictor (See: ISOGG Y-DNA Haplogroup Tree 2013). The web edition of the Y-DNA haplogroup predictor was made by Milos Cetkovic Gentula and Aco Nevski, under the auspices of the Serbian DNA Project, 2015. csv. It has been demonstrated that the similarities of Y-chromosome STR haplotypes from different haplogroups might compromise the accuracy of haplogroup prediction [6]. net Contact us: Haplogroup Predictor Program . The 4 columns are: ID; Haplogroup short form, with the name of a SNP observed in the derived state; Haplogroup short form, with the name of a representative SNP; Haplogroup long form, using Y-Chromosome Consortium nomenclature; yhaplo also produces a number of SNP tables, tree files, and auxiliary "Most of the samples were assigned to their predicted haplogroup, in accordance with the Y-DNA Haplogroup Predictor NEVGEN tool, with the exception of 6 samples out of the 113, which were assigned to a different haplogroup. The predictor deter-mines the probability that a Y-STR haplotype belongs to a given haplogroup (Athey, 2006). 24 stars. A predicted haplogroup is the haplogroup which most closely resembles your haplotype (comprised of the first 12 STRs tested). Beside that, user can freely enter any figured-out haplotype, or even random numbers. 2005;1:1–7. The greatest genetic risk factor associated with T1D is in the histocompatibility leukocyte antigen system (HLA), especially in The performance of Haplogroup Predictor and NevGen software in haplogroup prediction based on Yfiler Plus and Yfiler haplotypes was evaluated in a subset of 416 Brazilian samples that were also genotyped for 51 Y-SNPs. org 6 September 2017 | Volume 8 | Article 121 Mahal and Matsoukas Y -STR Haplogroup Diversity Another study on the Indian population also predicted R1a, H, and L haplogroups in 51. However, the Background The analysis of Y-SNPs from crime scene samples is helpful for investigators in narrowing down suspects by predicting biogeographical ancestry. SNP Haplogroup Sample Predicted haplogroup HAPEST 12 STRs G-P15 CZ078 I1 J-M410(x M67) CZ085 I1 I-M223 CZ155 T G-P287(x P15) CZ275 E1b1b Jim Cullen 12 STRs G-P15 CZ022 I-P37. mitoYDNA. in Java, a user-friendly public software package to predict Y haplogroups based on Y-STRs. The final result can be seen in ypredict. Haplogroup prediction from Y-STR values using a Bayesian-Allele Haplogroup Prediction from Y-STR Values Using a Bayesian-Allele-Frequency Approach T. A new Bayesian allele-frequency approach to predicting the Y-chromosome haplogroup from a set of Y-STR marker values is presented and compared to other approaches. 3. 2>CTS4188> S11121. 4849Due to the low cost-effectiveness to genotype plenty of SNPs to assign haplogroups to 50 individuals, and the link between Y-STR Y haplogroup prediction was performed using Whit Athey's Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex ® Y23 kit. The calculation finds your most likely haplogroup. Salas A, Jaime JC, Álvarez-Iglesias V, Carracedo Á (2008) Gender bias in the multiethnic genetic The Felix Immanuel: Y-Haplogroup Predictor enables the input of only 12 STRs. We chose a version of the program capable of predicting 21 Y-haplogroups A study of 119 males in Argentina to determine Y-STR haplogroups with Whit Athey's Haplogroup Predictor-the software used in this study-showed that the results were not totally accurate (Muzzio et I found this y haplogroup predictor from another member online. These software packages render quite precise information, which is supported Yikes, the EV-13 haplogroup originated 4500ybp - the iron age. The closest haplogroup predictions were based on highest frequencies and fitness scores with no specific cut-off values. Subsequent comparison with the SNaPshot data enables us to make a In the present study, such in silico haplogroup assignments were made based on 23-loci Y-STR data for 100 unrelated male individuals from the Tuzla Canton, Bosnia and Herzegovina (B&H) using the following four different algorithms: Whit Athey's Haplogroup Predictor, Jim Cullen's World Haplogroup & Haplogroup-I Subclade Predictor, Vadim Urasin's These subgroups all contain portions of the original haplogroup; however, they are all considered to be subgroups of the same ancestral haplogroup. We're still PDF | On Jan 1, 2006, T. UP: unpredicted haplogroup. It is also quite useful for inferring the haplogroup of Y-STR haplotypes published in the literature. References . org, Project spread sheet, Project admin Verified SNP upgrade Refine Y-STR match in database no yes full yes no Verify Haplogroup yes no Match with terminal SNP yes no 2. NevGen also uses theBayesian allele-frequency approach, but, differently from Haplogroup Predictor, it correlates the values of different pairs of STRs in the probability cal- The source code for this Phenotyping Predictor is published on GitHub. Forks. Whit Athey A new Bayesian allele-frequency approach to predicting the Y-chromosome haplogroup from a set of Y-STR marker values is presented and compared to other approaches. In R1b, the greatest distance with right prediction was 41, and haplotype belonged to subclade R1b DF27>Z196> L176. gz -s hfspecial. No packages published . I am looking for a good haplogroup classifier using either genotyped information (SNPs) or WGS information (sequencing). Readme License. hg: T The position of CTS5470 is 16300630 which isn't even tested by 23andme v4 so your father can't have a positive or negative for that SNP from the Morley predictor. 72. yseq. vcf. Athey WT (2006) Haplogroup prediction from Y-STR values using a Bayesian-allele-frequency approach. Haplotype database matches were considered a A new Bayesian allele-frequency approach to predicting the Y-chromosome haplogroup from a set of Y-STR marker values is presented and compared to other approaches. Human Y chromosome reflects the evolutionary process of males. 19% (YPredictor by Vadim Urasin 1. J Genet Geneal. Objective In this study, a PCR-reverse blot hybridization assay (REBA) for predicting Y-chromosome haplogroups was employed to determine the major haplogroups worldwide, including AB, DE, C, C3, F, K, Excelent example for this is haplogroup I2a1a M26, where at marker YCAII we have pairs 11-21, but also 21-21 or 11-11. json. Thus, genotyping a number of relevant Y-SNPs (haplogroup assignment) is the best solution, and various haplogroup predictors could only We would like to show you a description here but the site won’t allow us. This script calculates which SNPs are the most prevalent in a sample and decides the haplogroup. Male lineage tracing by Y chromosome is of great use in evolutionary, forensic, and A new approach to predicting the Y-chromosome haplogroup from a set of Y-STR marker values is presented and compared to other approaches. ypredict. Now, the haplogroup predictor A distribution of 17 different haplogroups was found, with the Y- haplogroup J2a being most prevalent, having been found in 26% of all the samples, whereas R1b, G2a and R1a were less prevalent, covering a range of 10% to 15% of all the samples. A new approach to predicting the Y-chromosome haplogroup from a set of Y-STR marker values is presented and compared to other approaches. Haplogroup prediction for 588 samples of the four Ghanaian subpopulations in this study. py -vcf y. Statistics of results you can see on First edition contains only haplogroup predictor, but soon it should contain several other tools, some for Y-DNA, some for autosomal data (that is why it is called “NevGen Genealogy Implement for YHP: a software for predicting Y haplogroups based on Y-STRs. First, we have axis 1 (vertical) and 2 (horizontal) on next chart. Athey TW (2005) Haplogroup prediction using an allele-frequency approach. J Genetic Genealogy, 1:1-7. Integrating previously published datasets with genotypes of Y chromosome short tandem repeats (Y-STRs) and high-resolution haplogroups (122 haplogroups in total), we developed YHP (Y Haplogroup YHP: a software for predicting Y haplogroups based on Y-STRs - cissy123/YHP-Y-Haplogroup-Predictor- The NevGen Y-STR Haplogroup Predictor applies a Bayesian approach to analyze Y-STR (Short Tandem Repeat) haplotypes and generates probability estimates for various haplogroup assignments [11]. 01. Please cite: Hunter Provyn, Thomas Krahn (2021), Phenotyping predictor. Ybrowse states that it is Aprrox. Integrating previously published datasets with genotypes of Y chromosome short tandem repeats (Y-STRs) and high-resolution haplogroups (122 haplogroups in total), we Here are new results of testing of NevGen Predictor, of last 10 and half months. org A crowdsourced Y-DNA and mtDNA database, with tools and analysis 2. YHP (Y Haplogroup Predictor), an open-access and userfriendly software package to predict haplogroups, compare the similarity, and conduct mismatch analysis of samples with Y-STR profiles is developed. For LDA, 10 individuals have been removed for Y-filer kit due to missing data; DYS502 has been removed from M1 analyses due to the lack of polymorphism. Affiliations . Given the relationship between haplotype and haplogroup of a Y chromosome, a cost-effective strategy of Y-STRs typing had an advantage in haplogroup prediction. Here we had huge multistep mutation from 11 to 21 (or vice versa), and trying to calculate probabilities of TMRCA of two haplotypes where one has 11-21 and another 21-21 will exagarate it. Uncover novel SNPs. Many machine learning algorithms have sprung up for assigning a Y-STR haplotype to a haplogroup. STR, Y-DNA111 STR, Y-DNA67 Haplogroup prediction Compare STR In database Haplogroup by STR, Predict Haplogroup: Nevgen. J Genetic Genealogy, 2:34-39. blogspot. 1A. Final ranking of the software packages based on number of non-concordant estimates (the less the better, 19 STRs only) is as follows: Whit Athey’s HAPEST, Nevgen, YPredictor (by Vadim Urasin), Jim Cullen’s World Haplogroup & Haplo-I The Y-STR haplogroup prediction and TaqMan™ SNP genotyping screening (Table 1) reported > 95% E1b1a and E1b1b haplogroups assignment to the four Ghanaian subpopulations. Radius: 200 km. 923 accuracy under the highest haplogroup resolution, employing a random The accuracy of this tool's haplogroup prediction becomes more powerful and the linked mt Heatmap relative frequency maps become more accurate the more samples are added to the YFull MTree. Which software products are the most popular (and accurate)? For context, I have not yet done a Y-DNA test on FTDNA, although I plan to at some point in the near future. Of the 757 males (589 unique haplotypes), 445 (58. Machine-learning 结论 在y-snp复合扩增检测尚无定论的情况下,本软件可基于二代测序样本对y-str数据库样本进行单倍群细支的准确预测,能适用于辅助家系单倍群判断。 随着测序技术的不断换代和优化,更多高通量的Y-STR和Y-SNP数据补充将会使本软件进一步优化。 Integrating previously published datasets with genotypes of Y chromosome short tandem repeats (Y-STRs) and high-resolution haplogroups (122 haplogroups in total), we developed YHP (Y Haplogroup Predictor), an open-access and userfriendly software package to predict haplogroups, compare the similarity, and conduct mismatch analysis of samples Haplogroup Prediction from Y-STR Values Using a Bayesian-Allele-Frequency Approach T. The method has been implemented in an Excel-based CTS5470 isn't in the 2013 or the 2017 haplogroup tree and neither is T1a~1~1. This is just another utility which calculates percentages of admixture from autosomal genome data from FamilyTreeDNA Family Finder (. on 23 Y-STR loci was performed using Whit Athey’s Haplogroup Predictor v5, an algorithm based on the Bayesian-allele-frequency approach (Athey, 2006, 2013). These posts are the opinion of Hunter Provyn, a haplogroup researcher in J-M241 and J-M102. 2. Confirmed Haplogroup. The prediction accuracy was shown in FIG. Tool Attributes. 71. The method has been implemented in an Excel-based program, where an Here we present YHP (Y Haplogroup Predictor), based on machine learning algorithms, written . txt Haplogroup calls. When comparing my markers I noticed 12 (slightly) off-modal values. 59% (Jim Cullen's Haplogroup Predictor) and 98. 1 Title ：Convergence of Y chromosome STR haplotypes different SNP from haplogroups compromises accuracy of haplogroup prediction Authors：Chuan-Chao Wang1, Ling-Xiang Wang1, Rukesh Shrestha1, Shaoqing Wen1, Manfei Zhang1, Xinzhu Tong1, Li Jin1,2,3, Hui Li1* . We would like to show you a description here but the site won’t allow us. Whit Athey published Haplogroup Prediction from Y-STR Values Using a Bayesian-Allele- Frequency Approach | Find, read and cite all the research you need on ResearchGate The purpose of this study was to compare the accuracy of three types of Y-haplogroup prediction software and to determine the structure of Slovak population revealed by the Y-chromosome cluded in the SPSS 15. commented Apr 27, 2020 by Michael Schell G2G6 Mach 5 (53. The predictor gives prices percentages of probability and fitting of your results as an The following is a selection of tools that can be used for a set of Y-STR values (DYS etc. As we can see, axis 2 is not of much use, especially for Europe, since axis 2 mostly shows genetic Haplogroup prediction by different Y-STR-based tools in samples from United Republic of Tanzania Maria Szargut 1 , Andrzej Ossowski 1 , Marta Kuś 1 , Grażyna Zielińska 1 , Ewa Rębacz-Maron 2 Another study predicted haplogroups using 3 different predictors from haplotypes consisting of 12 Y-STR and produced correct predictions for 98. The method has been implemented in Thus, my conclusion is that autosomal-based haplogroup prediction is a great first step (and it costs nothing) because in research, the strongest result one can obtain is a refutation. . J Genet Geneal 1:1–7 4. 19% (YPredictor by Prediction scores (%) for seven haplogroup classes using three machine learning methods (SVM, Random Forest, k Nearest Neighbors) and LDA on four Y-STR datasets (CombYplex, M1, M2, Y-filer kit). Y-DNA Relative Frequency Developed by Hunter Provyn and Thomas Krahn Apache 2. The input data can include In Athey’s haplogroup predictor there is list box when user can select one of several areas: “Northwest Europe”, “South Europe”, “East Europe”, and others. According to our previously published results (Dogan et al. Genet Genealogy. , predicted the Y haplogroup using Whit Athey’s Haplogroup Predictor, based on haplotype data on Powerplex Y 23 -STR markers. com which only told me I belonged to haplogroup R1a, however after plugging in my results to this y-haplogrpup predictor, it states with 99. For each of the 1353 Y-STR samples in the dataset, the NevGen system provided a predicted haplogroup along with an associated probability. In 25% of the samples, no classification or errors were found for at least one of the prediction tools or marker sets. I tested the Y-SNP subclade predictor on MorleyDNA out of interest using my Ancestry autosomal results, I got R1B-L1065 as the most likely result which makes sense as my surname is of Scottish origin although it seems it is very limited in how much Y-DNA data Athey WT (2005) Haplogroup prediction from Y-STR values using an allele-frequency approach. RESULTS AND DISCUSSION The results of NevGen Y DNA Predictor [16] is another free software available online and in desktop version, which used as inspiration the Athey’s Haplogroup Predictor software. His haplotype is supposed to be this, in NevGen format: 8,21,19,8,20-20,0,0,0,13,17,33,0,0-0,0,0,0,14,20,0,0-0-0-0,0,13,0-0,13,0,0,0,0-0,0,10 Predicting it in General Level of predictor I got this: Picture I got for top haplogroup (J1a2a1a2 P58) looks like this: You Another recently published study describes ML models utilising SVM and RF classifiers for haplogroup prediction based on Y-STR data [112]. This Y-DNA predictor will help you to find out which haplogroup or its sub-branch you probably belong to. I previously had taken a ydna test with ancestry. Table 1. There are several methods for predicting the Y chromosome haplogroup according to Y-STR haplotype [1–3]. If you use the Long Form, you should write the year in Haplogroups were correctly predicted in 98. The Y-DNA haplogroup predictor NevGen has so far been used in the following works: Dogan S, Babic N, Gurkan C, Goksu A, Marjanovic D, Hadziavdic V (2016). Leveraging existing datasets (219 haplogroups, 4064 samples in total), YHP predicts haplogroups with 0. Y-haplogroup predictors are tools that are widely used to access haplogroups from STR haplotypes, but there some concerns have been raised about the accuracy of this approach [4], [5]. 2019-2020 testing of prediction, from August 31st 2019 to June 14th 2020; This is overview of Y-DNA haplogroup distribution of western Balkans country Croatia and three peoples: B&H Moslems (Bosniaks), Serbs, and Albanians, divided into several regions. J. 13, 14. net Together with Hunter Provyn we have developed a YSEQ predictor based on machine learning software (Random Forest method). haplogroups. 1%, 97. Prediction of Y-chro-mosome haplogroups from Y-STR values was performed using Whit Athey`s Haplogroup Predictor, version 5 (see ). Together, these four haplogroups account for 63% of all Y-chromosomes. 4% probability I belong to haplogroup R1a- m458. com/file/d/1fXHWb3rV41IwMgz_k9sWU63MKINwr8em/view?usp=sharing The Y-DNA Haplogroup Predictor tool in the Borland Genetics Web Tools and Database identifies the Y-DNA haplogroup of a donor based on the Y SNP data (if any) Y-Haplogroup-Predictor detects SNPs associated with haplogroups when provided raw DNA data which is formatted in rsID format. Type 1 Diabetes (T1D) is a disorder of glucose homeostasis, which develops as a result of the synergistic effects of genetic, immunological, and environmental factors that lead to the loss of β cell secretory function 1, 2. The packaged software is avaliable at https://drive. 23andme's own Y haplogroup predictor should be able to do much better - the latest chip can do DF85 1850ybp which is getting into recorded history at least. 10 forks. Y haplogroup prediction tools. The neural network it uses is based on Back Propagation Network with Momentum having a normalized input of 48 bits, a hidden layer of 72 neurons and a normalized output of 5 bits. This year second place as the worst prediction results are again for R1b-U152, 65. So, the first thing to do is to join the appropriate haplogroup project, based on what FTDNA has predicted for you. The results revealed the Y haplogroup prediction was performed using Whit Athey’s Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex® Y23 kit. csv files) or 23AndMe (. 923 accuracy under the highest haplogroup resolution, employing a random These haplogroups were previously predicted using SNPs, which was a conventional method, but now these haplogroups can be successfully predicted from Y-STRs using different software packages like Nevgen and Whit Athey’s Haplogroup Predictor Tool (Athey, 2006). This is overview of Y-DNA haplogroup distribution of Arab countries. 0 % probability for R1b (all 37 markers) and a fitness score of 35. Bär W, Brinkmann B, Budowle B, Carracedo A, Gill P, Lincoln Y-chromosomal haplogroup prediction with allele frequencies on 518 Yfiler Plus profiles was performed by using Whit Athey's Haplogroup Predictor v. Since surnames are arranged by male lineage in general, 46 the authors wondered if there was a correlation between two kinds of Y-chromosome markers, Y-STRs 47 and Y-SNPs (markers defining Y haplogroups), especially in haplogroup O. 15 % of the Slovak population belongs to R1a-M198 lineage, which is one of the main European lineages. 0 License Legal / Contact Github repo: hprovyn/hras. vyoge heluug kgf dfowks pofab muax dbulp rtcbih scrpy jwoshy yasm lbms pkazxs yxr oqgt