Excap: maximization of haplotypic diversity of linked markers.

Autor: André Kahles, Fahad Sarqume, Peter Savolainen, Lars Arvestad

Publikováno v: PLoS ONE, Vol 8, Iss 11, p e79012 (2013)

Genetic markers, defined as variable regions of DNA, can be utilized for distinguishing individuals or populations. As long as markers are independent, it is easy to combine the information they provide. For nonrecombinant sequences like mtDNA, choos

Externí odkaz: https://doaj.org/article/42df63ee49d24ddca4cade1d4791ade0

The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants

Autor: Bastian Schiffthaler, Ian M. Møller, Olivier Keech, Yrin Eldfjell, Lars Arvestad, Lisa Öberg, Nathaniel R. Street, Alexis R. Sullivan, Xiao-Ru Wang, Kim H. Hebelstrup, Nicolas Delhomme, Torben Asp

Publikováno v: Sullivan, A R, Eldfjell, Y, Schiffthaler, B, Delhomme, N, Asp, T, Hebelstrup, K, Keech, O, Öberg, L, Møller, I M, Arvestad, L, Street, N R & Wang, X-R 2020, ' The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants ', Genome Biology and Evolution, vol. 12, no. 1, pp. 3586-3598 . https://doi.org/10.1093/gbe/evz263
Genome Biology and Evolution

Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comp

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1836079fc24739163de3cf7b16339e36
https://pub.epsilon.slu.se/16955/

RecPhyloXML : a format for reconciled gene trees

Autor: Vincent Berry, Guillaume Gence, Bastien Boussau, Lars Arvestad, François Chevenet, Adrián A. Davín, Gergely J. Szöllősi, Damir Hasic, Diego Mallo, Celine Scornavacca, Nicolas Comte, Louxin Zhang, Vincent Daubin, David Posada, David Dylus, Eric Tannier, Christophe Dessimoz, Anne-Muriel Arigon Chifolleau, Rémi Planel, Wandrille Duchemin, Mukul S. Bansal

Publikováno v: Bioinformatics
Bioinformatics, 2018, 34 (21), pp.3646-3652. ⟨10.1093/bioinformatics/bty389⟩
Bioinformatics, Oxford University Press (OUP), 2018, 34 (21), pp.3646-3652. ⟨10.1093/bioinformatics/bty389⟩
Bioinformatics, vol. 34, no. 21, pp. 3646-3652

Motivation A reconciliation is an annotation of the nodes of a gene tree with evolutionary events—for example, speciation, gene duplication, transfer, loss, etc.—along with a mapping onto a species tree. Many algorithms and software produce or us

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::16d9963ac80f7dbba153bec8a9b5c1e2
http://www.documentation.ird.fr/hor/fdi:010074453

Probabilistic inference of lateral gene transfer events

Autor: Lars Arvestad, Mehmood Alam Khan, Owais Mahmudi, Jens Lagergren, Ikram Ullah

Publikováno v: BMC Bioinformatics

Background Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cb6849ae26621c1d7b2feed55ceb649c
https://doi.org/10.1186/s12859-016-1268-2

Structural variation detection with read pair information --- An improved null-hypothesis reduces bias

Autor: Kristoffer Sahlin, Lars Arvestad, Mattias Frånberg

Reads from paired-end and mate-pair libraries are often utilized to find structural variation in genomes, and one common approach is to use their fragment length for detection. After aligning read-pairs to the reference, read-pair distances are analy

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::246638cc89e5e21446ad992a940fab5f
https://doi.org/10.1101/036707