In the life sciences, FAIR principles have reshaped research policy, but their implementation still relies largely on individual researchers – many of whom lack the expertise or support needed to make...

In the life sciences, FAIR principles have reshaped research policy, but their implementation still relies largely on individual researchers – many of whom lack the expertise or support needed to make...

Rob Waterhouse has always been fascinated by life’s many interconnections, from his childhood on an isolated ranch in Swaziland to his current role leading a community of more than 1,100 researchers a...

In phylogenomics, gene tree reconstruction depends on multiple sequence alignment (MSA) and tree inference, and ongoing work continues to improve inference quality. Denser taxon sampling has been associated with improved gene tree inference, suggesting that adding homologs could be a practical route to higher accuracy as sequence databases continue to expand. However, adding sequences can influence multiple steps of typical inference pipelines, and little is known on its specific effect on the multiple sequence alignment, tree reconstruction, and rooting steps. We performed a large-scale empirical benchmark to quantify how homolog enrichment affects alignment and phylogenetic inference. Using an enrichment-impoverishment design and a measure of tree accuracy based on taxonomic congruence, we found that enrichment consistently improves tree inference quality, while effects on alignment quality are marginal. We show that this improvement is associated with accurate root placement on enriched trees when sensitive homolog search is accompanied. Notably, much of the benefit can be retained with relatively compact alignments produced by sequence addition. Building on these observations, we provide a tool, AmpliPhy, which efficiently improves phylogenetic reconstruction of protein families through homolog enrichment. The AmpliPhy open-source pipeline software is available at https://github.com/DessimozLab/ampliphy. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, https://ror.org/00yjd3n13, 216623, 10005715

Treponematosis, a bacterial infection caused by Treponema pallidum subspecies and T. carateum (yaws, bejel, syphilis, pinta), has afflicted humans for millennia. Despite paleopathological evidence and...

YouTube video by Département de Biologie Computationnelle - UNIL

EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

A total of eight expertly curated knowledgebases developed by SIB scientists are now designated as ELIXIR Core Data Resources (CDRs) – with the three new additions representing half of those sel...

Critics say “autocratic” behavior by GISAID could hamper response to a future pandemic

The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...

We are deeply saddened to announce the passing of our co-founder and Group Leader Amos Bairoch. Emeritus professor at the University of Geneva, he shaped the development of bioinformatics over more th...