Buxus and Tetracentron genomes help resolve eudicot genome history
Ancient whole-genome duplications (WGDs) characterize many large angiosperm lineages,
including angiosperms themselves. Prominently, the core eudicot lineage accommodates …
including angiosperms themselves. Prominently, the core eudicot lineage accommodates …
AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories
AsymmeTree is a flexible and easy-to-use Python package for the simulation of gene family
histories. It simulates species trees and considers the joint action of gene duplication, loss …
histories. It simulates species trees and considers the joint action of gene duplication, loss …
From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes
Q Xu, L Jin, C Zheng, X Zhang, J Leebens-Mack… - Scientific Reports, 2023 - nature.com
To reconstruct the ancestral genome of a set of phylogenetically related descendant
species, we use the raccroche pipeline for organizing a large number of generalized gene …
species, we use the raccroche pipeline for organizing a large number of generalized gene …
Ancestral flowering plant chromosomes and gene orders based on generalized adjacencies and chromosomal gene co-occurrences
Recurrent whole genome duplication and the ensuing loss of redundant genes—
fractionation—complicate efforts to reconstruct the gene orders and chromosomes of the …
fractionation—complicate efforts to reconstruct the gene orders and chromosomes of the …
RACCROCHE: Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-occurrences
Given the phylogenetic relationships of several extant species, the reconstruction of their
ancestral genomes at the gene and chromosome level is made difficult by the cycles of …
ancestral genomes at the gene and chromosome level is made difficult by the cycles of …
Gene order phylogeny via ancestral genome reconstruction under dollo
Q Xu, D Sankoff - RECOMB International Workshop on Comparative …, 2023 - Springer
We present a proof of principle for a new kind of stepwise algorithm for unrooted binary gene-
order phylogenies. This method incorporates a simple look-ahead inspired by Dollo's law …
order phylogenies. This method incorporates a simple look-ahead inspired by Dollo's law …
The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny
Q Xu, X Zhang, Y Zhang, C Zheng… - … of Bioinformatics and …, 2021 - World Scientific
Using RACCROCHE, a method for reconstructing gene content and order of ancestral
chromosomes from a phylogeny of extant genomes represented by the gene orders on their …
chromosomes from a phylogeny of extant genomes represented by the gene orders on their …
[PDF][PDF] The design, implementation and application of a computational pipeline for the reconstruction of the gene order on the chromosomes of very ancient ancestral …
Q Xu - 2023 - ruor.uottawa.ca
This thesis presents a novel approach to reconstructing ancestral genomes of a number of
descendant species related by a phylogeny. Traditional methods face challenges due to …
descendant species related by a phylogeny. Traditional methods face challenges due to …
[PDF][PDF] AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories. Software 2022, 1, 276–298
AsymmeTree is a flexible and easy-to-use Python package for the simulation of gene family
histories. It simulates species trees and considers the joint action of gene duplication, loss …
histories. It simulates species trees and considers the joint action of gene duplication, loss …
AsymmeTree
Abstract (EN) AsymmeTree is a flexible and easy-to-use Python package for the simulation
of gene family histories. It simulates species trees and considers the joint action of gene …
of gene family histories. It simulates species trees and considers the joint action of gene …