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FRANz: Reconstruction of wild multigeneration pedigrees
"... Summary: We present a software package for pedigree reconstruction in natural populations using codominant genomic markers such as microsatellites and SNPs. If available, the algorithm makes use of prior information such as known relationships (subpedigrees) or the age and sex of individuals. Stat ..."
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Summary: We present a software package for pedigree reconstruction in natural populations using codominant genomic markers such as microsatellites and SNPs. If available, the algorithm makes use of prior information such as known relationships (subpedigrees) or the age and sex of individuals. Statistical confidence is estimated by MCMC sampling. The accuracy of the algorithm is demonstrated for simulated data as well as an empirical data set with known pedigree. The parentage inference is robust even in the presence of genotyping errors. Availability: The C source code of FRANz can be obtained under the
Pedigree reconstruction using identity by descent. Class project,
, 2008
"... Abstract. Can we find the family trees, or pedigrees, that relate the haplotypes of a group of individuals? Collecting the genealogical information for how individuals are related is a very timeconsuming and expensive process. Methods for automating the construction of pedigrees could streamline ..."
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Cited by 6 (2 self)
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Abstract. Can we find the family trees, or pedigrees, that relate the haplotypes of a group of individuals? Collecting the genealogical information for how individuals are related is a very timeconsuming and expensive process. Methods for automating the construction of pedigrees could streamline this process. While constructing singlegeneration families is relatively easy given whole genome data, reconstructing multigenerational, possibly inbred, pedigrees is much more challenging. This paper addresses the important question of reconstructing monogamous, regular pedigrees, where pedigrees are regular when individuals mate only with other individuals at the same generation. This paper introduces two multigenerational pedigree reconstruction methods: one for inbreeding relationships and one for outbreeding relationships. In contrast to previous methods that focused on the independent estimation of relationship distances between every pair of typed individuals, here we present methods that aim at the reconstruction of the entire pedigree. We show that both our methods outperform the stateoftheart and that the outbreeding method is capable of reconstructing pedigrees at least six generations back in time with high accuracy. The two programs are available at
Algorithms for comparing pedigree graphs
 CoRR
"... Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic data from a set of extant individuals and reconstruct ancest ..."
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Cited by 3 (3 self)
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Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic data from a set of extant individuals and reconstruct ancestral individuals. There is a great need to evaluate the quality of these methods by comparing the estimated pedigree to the true pedigree. In this paper, we consider two main pedigree comparison problems. The first is the pedigree isomorphism problem, for which we present a lineartime algorithm for leaflabeled pedigrees. The second is the pedigree edit distance problem, for which we present 1) several algorithms that are fast and exact in various special cases, and 2) a general, randomized heuristic algorithm. In the negative direction, we first prove that the pedigree isomorphism problem is as hard as the general graph isomorphism problem, and that the subpedigree isomorphism problem is NPhard. We then show that the pedigree edit distance problem is APXhard in general and NPhard on leaflabeled pedigrees. We use simulated pedigrees to compare our editdistance algorithms to each other as well as to a branchandbound algorithm that always finds an optimal solution.
IPED2: Inheritance Path based Pedigree Reconstruction Algorithm for Complicated Pedigrees
"... Motivation: Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. The problem is known to be NPhard even for datasets known to only contain siblings. Some recent methods have been developed to accurately and efficiently reconstr ..."
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Motivation: Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. The problem is known to be NPhard even for datasets known to only contain siblings. Some recent methods have been developed to accurately and efficiently reconstruct pedigrees. These methods, however, still consider relatively simple pedigrees, for example, they are not able to handle halfsibling situations where a pair of individuals only share one parent. Results: In this work, we propose an efficient method, IPED2, based on our previous work, which specifically targets reconstruction of complicated pedigrees that include halfsiblings. We note that the presence of halfsiblings makes the reconstruction problem significantly more challenging which is why previous methods exclude the possibility of halfsiblings. We proposed a novel model as well as an efficient graph algorithm and experiments show that our algorithm achieves relatively accurate reconstruction. To our knowledge, this is the first method that is able to handle pedigree reconstruction based on genotype data only when halfsibling exists in any generation of the pedigree.
Reconstructing pedigrees: some identifiability questions for a recombinationmutation model
 J. Math. Biol
, 2013
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unknown title
"... eRecombination Genetic drift Wright–Fisher model today that left no genetic trace – represent ‘ghost ’ ancestors in a strong sense. In this short note, we use simple analytical argument and simulations to estimate how many such individuals exist in finite Wright–Fisher populations. © 2015 Elsevier I ..."
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eRecombination Genetic drift Wright–Fisher model today that left no genetic trace – represent ‘ghost ’ ancestors in a strong sense. In this short note, we use simple analytical argument and simulations to estimate how many such individuals exist in finite Wright–Fisher populations. © 2015 Elsevier Inc. All rights reserved.
PROCEEDINGS Open Access Isomorphism and similarity for 2generation pedigrees
"... We consider the emerging problem of comparing the similarity between (unlabeled) pedigrees. More specifically, we focus on the simplest pedigrees, namely, the 2generation pedigrees. We show that the isomorphism testing for two 2generation pedigrees is GIhard. If the 2generation pedigrees are mon ..."
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We consider the emerging problem of comparing the similarity between (unlabeled) pedigrees. More specifically, we focus on the simplest pedigrees, namely, the 2generation pedigrees. We show that the isomorphism testing for two 2generation pedigrees is GIhard. If the 2generation pedigrees are monogamous (i.e., each individual at level1 can mate with exactly one partner) then the isomorphism testing problem can be solved in polynomial time. We then consider the problem by relaxing it into an NPcomplete decomposition problem which can be formulated as the Minimum Common Integer Pair Partition (MCIPP) problem, which we show to be FPT by exploiting a property of the optimal solution. While there is still some difficulty to overcome, this lays down a solid foundation for this research.
Advance Access publication September 18, 2014 How Much Information is Needed to Infer Reticulate Evolutionary Histories?
"... which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. ..."
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which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Historical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE)
, 2014
"... Recent technological improvements in the field of genetic data extraction give rise to the possibility of reconstructing the historical pedigrees of entire populations from the genotypes of individuals living today. Current methods are still not practical for real data scenarios as they have limited ..."
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Recent technological improvements in the field of genetic data extraction give rise to the possibility of reconstructing the historical pedigrees of entire populations from the genotypes of individuals living today. Current methods are still not practical for real data scenarios as they have limited accuracy and assume unrealistic assumptions of monogamy and synchronized generations. In order to address these issues, we develop a new method for pedigree reconstruction, PREPARE, which is based on formulations of the pedigree reconstruction problem as variants of graph coloring. The new formulation allows us to consider features that were overlooked by previous methods, resulting in a reconstruction of up to 5 generations back in time, with an order of magnitude improvement of falsenegatives rates over the state of the art, while keeping a lower level of false positive rates. We demonstrate the accuracy of PREPARE compared to previous approaches using simulation studies over a range of population sizes, including inbred and outbred populations, monogamous and polygamous mating patterns, as well as synchronous and asynchronous mating.