Results 241 to 250 of about 101,371 (270)

Reconciliation With Nonbinary Gene Trees Revisited

Journal of the ACM, 2014
By reconciling the phylogenetic tree of a gene family with the corresponding species tree, it is possible to infer lineage-specific duplications and losses with high confidence and hence to annotate orthologs and paralogs. The currently available reconciliation methods for nonbinary gene trees are computationally expensive for genome-scale
Yu Zheng, Louxin Zhang
openaire   +1 more source

Reconciliation of a gene network and species tree

Journal of Theoretical Biology, 2019
The phylogenetic trees of genes and the species which they belong to are similar, but distinct due to various evolutionary processes which affect genes but do not create new species. Reconciliations map the gene tree into the species tree, explaining the discrepancies by events including gene duplications and losses.
Yao-ban Chan, Charles Robin
openaire   +2 more sources

SPR-BASED TREE RECONCILIATION: NON-BINARY TREES AND MULTIPLE SOLUTIONS

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2007
The SPR (subtree prune and regraft) operation is used as the basis for reconciling incongruent phylogenetic trees, particularly for detecting and analyzing non-treelike evolutionary histories such as horizontal gene transfer, hybrid speciation, and recombination.
CUONG THAN, LUAY NAKHLEH
openaire   +1 more source

Tree Reconciliation: Reconstruction of Species Phylogeny by Phylogenetic Gene Trees

Molecular Biology, 2002
It is well known that phylogenetic trees derived from different protein families are often incongruent. This is explained by mapping errors and by the essential processes of gene duplication, loss, and horizontal transfer. Therefore, the problem is to derive a "consensus" tree best fitting the given set of gene trees. This work presents a new method of
V. V. V'yugin, M. S. Gelfand, V. A. Lyubetsky   +2 more
openaire   +1 more source

Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees

2017
Phylogenetic tree reconciliation is a widely used approach for analyzing the inconsistencies between the evolutionary histories of genes, and the species through which they have evolved. An important aspect of tree reconciliation are the cost functions involved that are the minimum number of evolutionary events explaining such inconsistencies.
Paweł Górecki, Alexey Markin, Agnieszka Mykowiecka, Jarosław Paszek, Oliver Eulenstein   +4 more
openaire   +1 more source

A Tool for Non-binary Tree Reconciliation

2013
Tree reconciliation has been widely used to study the important roles of gene duplication and loss, and to infer a species tree from gene trees in evolutionary biology. Motivated by the fact that both reference species trees and real gene trees are often non-binary, we develop a novel computer program to reconcile two non-binary trees.
Yu Zheng, Louxin Zhang
openaire   +1 more source

Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations

2008
We describe algorithms to explore the space of all possible reconciliations between a gene tree and a species tree. We propose an algorithm for generating a random reconciliation, and combinatorial operators and algorithms to explore the space of all possible reconciliations between a gene tree and a species tree in optimal time.
Jean-Philippe Doyon, Cedric Chauve, Sylvie Hamel   +2 more
openaire   +1 more source

[Tree reconciliation: reconstruction of species evolution by phylogenetic gene trees].

Molekuliarnaia biologiia, 2002
It is well known that phylogenetic trees derived from different protein families are often incongruent. This is explained by mapping errors and by the essential processes of gene duplication, loss, and horizontal transfer. Therefore, the problem is to derive a "consensus" tree best fitting the given set of gene trees. This work presents a new method of
V V, V'iugin, M S, Gel'fand, V A, Liubetskiĭ   +2 more
openaire   +1 more source

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

Nucleic Acids Research, 2021
Ivica Letunic, Peer Bork
exaly  

Sensitive protein alignments at tree-of-life scale using DIAMOND

Nature Methods, 2021
Benjamin Buchfink, Klaus Reuter, Hajk-Georg Drost   +2 more
exaly