Zobrazeno 1 - 10
of 278
pro vyhledávání: '"Holland Barbara R"'
Autor:
Soewongsono, Albert C., Diao, Jiahao, Stark, Tristan, Wilson, Amanda E., Liberles, David A., Holland, Barbara R., O'Reilly, Malgorzata M.
We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the species tree,
Externí odkaz:
http://arxiv.org/abs/2309.06447
In this work, we develop a stochastic model of gene gain and loss with the aim of inferring when (if at all) in evolutionary history and association between two genes arises. The data we consider is a species tree along with information on the presen
Externí odkaz:
http://arxiv.org/abs/2309.02813
There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the phylogenet
Externí odkaz:
http://arxiv.org/abs/2309.02788
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes underlying em
Externí odkaz:
http://arxiv.org/abs/2110.03907
Publikováno v:
BMC Evolutionary Biology, Vol 9, Iss 1, p 200 (2009)
Abstract Correction to Shavit Grievink L, Penny D, Hendy MD, Holland BR: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol 2008, 8(1):317.
Externí odkaz:
https://doaj.org/article/61c17a93afac4478968c99e68181559a
Publikováno v:
BMC Evolutionary Biology, Vol 8, Iss 1, p 317 (2008)
Abstract Background Commonly used phylogenetic models assume a homogeneous evolutionary process throughout the tree. It is known that these homogeneous models are often too simplistic, and that with time some properties of the evolutionary process ca
Externí odkaz:
https://doaj.org/article/a72709b3532140458f40429a248da6cd
Publikováno v:
BMC Evolutionary Biology, Vol 8, Iss 1, p 202 (2008)
Abstract Background A simple and widely used approach for detecting hybridization in phylogenies is to reconstruct gene trees from independent gene loci, and to look for gene tree incongruence. However, this approach may be confounded by factors such
Externí odkaz:
https://doaj.org/article/3d1a388e2995477498beadbdcfdbbf1f
Publikováno v:
BMC Bioinformatics, Vol 7, Iss 1, p 350 (2006)
Abstract Background Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP
Externí odkaz:
https://doaj.org/article/29038737b4244a56bf822e7cecf0b991
Publikováno v:
Journal of molecular evolution, 1-15 (2019)
The underlying structure of the canonical amino acid substitution matrix (aaSM) is examined by considering stepwise improvements in the differential recognition of amino acids according to their chemical properties during the branching history of the
Externí odkaz:
http://arxiv.org/abs/1912.05057
Publikováno v:
Journal of Mathematical Biology, 1-25 (2020)
A matrix Lie algebra is a linear space of matrices closed under the operation $ [A, B] = AB-BA $. The "Lie closure" of a set of matrices is the smallest matrix Lie algebra which contains the set. In the context of Markov chain theory, if a set of rat
Externí odkaz:
http://arxiv.org/abs/1804.11249