3 papers
quant-ph2026
Lossless Reductions and Hybrid Sampling for Phylogeny Using the Maximum Compatibility Criterion
Orson Ye, James Bonfield, Joshua Cudby +2
Maximum compatibility provides a criterion for phylogenetic reconstruction in which the objective is to retain a maximum set of mutually compatible characters. For binary character…
quant-ph2025
Pangenome-guided sequence assembly via binary optimisation
Josh Cudby, James Bonfield, Chenxi Zhou +2
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequen…
q-bio.GN2020
Twelve years of SAMtools and BCFtools
Petr Danecek, James K. Bonfield, Jennifer Liddle +8
Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago…