BadiRate: estimating family turnover rates by likelihood-based methods. - Pablo Librado; Filipe G. Vieira; Julio Rozas (Bioinform., 2012)

ngsTools: methods for population genetics analyses from next-generation sequencing data. - Matteo Fumagalli 002; Filipe G. Vieira; Tyler Linderoth; Rasmus Nielsen (Bioinform., 2014)

Estimating IBD tracts from low coverage NGS data. - Filipe G. Vieira; Anders Albrechtsen; Rasmus Nielsen (Bioinform., 2016)

BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines. - Yözen Hernández; Rocky Bernstein; Pedro E. Pagan; Levy Vargas; William McCaig; Girish Ramrattan; Saymon Akther; Amanda Larracuente; Lia Di; Filipe G. Vieira; Wei-Gang Qiu (BMC Bioinform., 2018)

ngsLD: evaluating linkage disequilibrium using genotype likelihoods. - Emma A. Fox; Alison E. Wright; Matteo Fumagalli 002; Filipe G. Vieira (Bioinform., 2019)