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Jan 16, 2023 · AGORA is an algorithm to reconstruct ancestral gene order. AGORA is a parsimony-based algorithm that estimates the content and order of genes in the ancestor of a group of extant species for which ...
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Jan 1, 2019 · We define a proxy gene as the most closely related descendant of that ancestral gene in an extant organism. One could in principle define ‘closest’ in different ways, but for convenience we define it in terms of protein sequence divergence, as this quantity is easily calculated from our trees as total branch length in the path from an ancestral gene to an extant (leaf) descendant.
- Xiaosong Huang, Xiaosong Huang, Laurent-Philippe Albou, Tremayne Mushayahama, Anushya Muruganujan, H...
- 10.1093/nar/gky1009
- 2019
- 2019/01/01
Ancestral reconstruction. Ancestral reconstruction (also known as Character Mapping or Character Optimization) is the extrapolation back in time from measured characteristics of individuals, populations, or species to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary ...
Jan 18, 2024 · In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies formalized in a structure called an ancestral recombination graph (ARG). An ARG extensively encodes the ancestry of the genome(s) and thus is replete with valuable ...
Apr 13, 2023 · Generating sets of long contigs. To infer gene content and gene order for each chromosome in each ancestral genome in a phylogeny, we identify a large number of generalized 11 (or “gapped” 12 ...
Jan 16, 2023 · For example, in this study we used gene trees to define the set of ancestral genes to be ordered into chromosomes and to locate the set of descendant genes in extant genomes (orthogroups). Although we showed that two different sources of orthogroups (Ensembl and OMA) generate essentially the same Boreoeutheria genome, this may be different for more ancient genomes or poorer-quality gene trees.
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What is the ancestral genome resource?
Are ancestral genomes a resource for reconstructed ancestral genes and chromosomes?
What is the difference between Agora and ancestral genomes?
Are ancestral genes eukaryotic?
Oct 17, 2018 · The Olfactores ancestor is the common ancestor of vertebrates and tunicates and the closest ancestor upstream of the reconstructed pre-1R genome in Ensembl gene trees. This set of ancestral genes provides a direct connection to the human genome, through their 8378 human descendent genes.
