Publications by authors named "Magali Semeria"
Article Synopsis
- Gene trees often struggle with weak support, but these issues can be improved by integrating information from species trees and genomic context.
- The new method called ProfileNJ enhances existing gene trees by correcting weak branches using species tree data and distance matrices, making it efficient enough to analyze large databases like Ensembl Compara.
- A web tool called RefineTree, which includes ProfileNJ and other gene tree correction methods, is now available for researchers to access and utilize for genomic analyses.
Prey aggregations, such as fish schools, attract numerous predators. This typically leads to the formation of multispecific groups of predators. These aggregations can be seen both as a place of increased competition and as a place of possible facilitation between predators.
View Article and Find Full Text PDFBackground: Most models of genome evolution concern either genetic sequences, gene content or gene order. They sometimes integrate two of the three levels, but rarely the three of them. Probabilistic models of gene order evolution usually have to assume constant gene content or adopt a presence/absence coding of gene neighborhoods which is blind to complex events modifying gene content.
View Article and Find Full Text PDFArticle Synopsis
- The study highlights how traditional gene trees can sometimes conflict with evolutionary information like conserved synteny, which can indicate gene relationships.
- The researchers developed polynomial-time algorithms to adjust these gene trees based on external orthology constraints, aiming to create a modified tree that remains as similar as possible to the original.
- Validity of these modifications was confirmed through likelihood ratio calculations, showing that the adjusted trees often have comparable statistical validity to the original trees.