PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. - Jaime Huerta-Cepas; Salvador Capella-Gutiérrez; Leszek P. Pryszcz; Ivan Andreevich Denisov; Diego Kormes; Marina Marcet-Houben; Toni Gabaldón (Nucleic Acids Res., 2011)

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. - Jaime Huerta-Cepas; Salvador Capella-Gutiérrez; Leszek P. Pryszcz; Marina Marcet-Houben; Toni Gabaldón (Nucleic Acids Res., 2014)

MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life. - Uciel Chorostecki; Manuel Molina; Leszek P. Pryszcz; Toni Gabaldón (Nucleic Acids Res., 2020)

ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. - Leszek P. Pryszcz; Eva Maria Novoa (Bioinform., 2021)