Reconstructing protein and gene phylogenies by extending the framework of reconciliation. - Esaie Kuitche; Aïda Ouangraoua (CoRR, 2016)

Aligning coding sequences with frameshift extension penalties. - Safa Jammali; Esaie Kuitche; Ayoub Rachati; François Bélanger; Michelle S. Scott; Aïda Ouangraoua (Algorithms Mol. Biol., 2017)

Improving spliced alignment for identification of ortholog groups and multiple CDS alignment. - Jean-David Aguilar; Safa Jammali; Esaie Kuitche; Aïda Ouangraoua (CoRR, 2017)

Reconstructing protein and gene phylogenies using reconciliation and soft-clustering. - Esaie Kuitche; Manuel Lafond; Aïda Ouangraoua (J. Bioinform. Comput. Biol., 2017)

SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups. - Safa Jammali; Jean-David Aguilar; Esaie Kuitche; Aïda Ouangraoua (BMC Bioinform., 2019)

SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution. - Esaie Kuitche; Safa Jammali; Aïda Ouangraoua (BMC Bioinform., 2019)

DoubleRecViz: a web-based tool for visualizing transcript-gene-species tree reconciliation. - Esaie Kuitche; Yanchun Qi; Nadia Tahiri; Jack Parmer; Aïda Ouangraoua (Bioinform., 2021)