3 citations · 7 across the 8 of their papers we have counts for
9 papers
Improving spliced alignment for identification of ortholog groups and multiple CDS alignment
Jean-David Aguilar, Safa Jammali, Esaie Kuitche +1
The Spliced Alignment Problem (SAP) that consists in finding an optimal semi-global alignment of a spliced RNA sequence on an unspliced genomic sequence has been largely considered…
Gene Tree Construction and Correction using SuperTree and Reconciliation
Manuel Lafond, Cédric Chauve, Nadia El-Mabrouk +1
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this…
Reconstructing protein and gene phylogenies by extending the framework of reconciliation
Esaie Kuitche, Manuel Lafond, Aïda Ouangraoua
The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single…
Aligning coding sequences with frameshift extension penalties
Safa Jammali, Esaie Kuitche, Ayoub Rachati +3
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative am…
The SCJ small parsimony problem for weighted gene adjacencies (Extended version)
Nina Luhmann, Manuel Lafond, Annelyse Thévenin +3
Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the…
Alignment of protein-coding sequences with frameshift extension penalties
François Bélanger, Aïda Ouangraoua
We introduce an algorithm for the alignment of protein- coding sequences accounting for frameshifts. The main specificity of this algorithm as compared to previously published prot…