EUCALYPT: efficient tree reconciliation enumerator
نویسندگان
چکیده
منابع مشابه
Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost
Polytomies in gene trees are multifurcated nodes corresponding to unresolved parts of the tree, usually due to insufficient differentiation between sequences. Resolving a multifurcated tree has been considered by many authors, the objective function often being the number of duplications and losses reflected by the reconciliation of the resolved gene tree with a given species tree. Here, we pre...
متن کاملUnifying Parsimonious Tree Reconciliation
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a ...
متن کاملPareto-optimal phylogenetic tree reconciliation
MOTIVATION Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is...
متن کاملGene tree species tree reconciliation with gene conversion
Gene tree/species tree reconciliation is a recent decisive progress in phylogenetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by gene-scale events such as duplication, loss, transfer, which translates mathematically into a mapping between gene tree nodes and species tree nodes or branche...
متن کاملBUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
MOTIVATION BUCKy is a C++ program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes. A population tree with branch lengths in coalescent units is estimated from quartet concordance factors. AVAILABILITY BUCKy is open s...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Algorithms for Molecular Biology
سال: 2015
ISSN: 1748-7188
DOI: 10.1186/s13015-014-0031-3