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Ultra-Perfect Sorting Scenarios., , and . RECOMB-CG, volume 6398 of Lecture Notes in Computer Science, page 50-61. Springer, (2010)Prediction of Contiguous Regions in the Amniote Ancestral Genome., , , , and . ISBRA, volume 5542 of Lecture Notes in Computer Science, page 173-185. Springer, (2009)Inferring Transcript Phylogenies from Transcript Ortholog Clusters., and . RECOMB-CG, volume 14616 of Lecture Notes in Computer Science, page 47-68. Springer, (2024)Orthology and Paralogy Relationships at Transcript Level., and . J. Comput. Biol., 31 (4): 277-293 (2024)aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences., and . Bioinform., 34 (13): i70-i78 (2018)Aligning coding sequences with frameshift extension penalties., , , , , and . Algorithms Mol. Biol., 12 (1): 10:1-10:18 (2017)SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution., , and . BMC Bioinform., 20-S (20): 640 (2019)The SCJ Small Parsimony Problem for Weighted Gene Adjacencies., , , , , and . IEEE ACM Trans. Comput. Biol. Bioinform., 16 (4): 1364-1373 (2019)Gene tree and species tree reconciliation with endosymbiotic gene transfer., , , and . Bioinform., 37 (Supplement): 120-132 (2021)Reconstructing protein and gene phylogenies using reconciliation and soft-clustering., , and . J. Bioinform. Comput. Biol., 15 (6): 1740007:1-1740007:25 (2017)