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

"Public health might be the greatest measure of kindness, the greatest measure of how to treat each other." - William Foege

The chair of a federal vaccine advisory panel charted a new course for the committee in a podcast released Thursday, questioning longstanding recommendations.

The United States has bribed and bullied the WHO from the earliest days of the organization.

It ain't normal

Disinformation Disinformation is false or misleading information created and spread to advance policy, political, economic or ideological goals. It is sometimes used by industries, governments, and ot...

The agency used to warn of chelation, used by RFK Jr.'s anti-vaccine ally David Geier.

Successful American action in Venezuela and threats against Greenland suggest the rules-based international order that emerged following the Second World War is now on life support.

The war in Sudan has transformed far more than its own frontlines. It has reshaped the security economies of its neighbours, activating new supply nodes and embedding weapons and combatants into cross...

The three remaining hunger strikers have been convicted of nothing. Yet with astonishing cruelty, ministers refuse to listen to their reasonable demands, says Guardian columnist George Monbiot

Or: what breaks me