Evidence map›Paper›PMID 41846951›Full record

ArticlebioRxiv : the preprint server for biology2026

CAPHEINE, or everything and the kitchen sink: a workflow for automating selection analyses using HyPhy.

Hannah Verdonk, Danielle Callan, Sergei L Kosakovsky Pond

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

3 authors.

Hannah VerdonkInstitute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, Pennsylvania, USA.ORCID 0000-0003-1967-4403
Danielle CallanInstitute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, Pennsylvania, USA.
Sergei L Kosakovsky PondInstitute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, Pennsylvania, USA.

Funding

An in integrated platform for multiomic analyses of pathogen and host data using scalable public infrastructureU24AI183870 · NIAID · PENNSYLVANIA STATE UNIVERSITY, THE · PI Kelsey M Beavers, Maximilian Haeussler · 2024 to 2026
$10.2M
Title: Functional Annotation of Genomes via Phenotypic Convergence within Large Multi-species AlignmentsR01HG009299 · NHGRI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Maria D Chikina, Nathaniel L Clark · 2017 to 2026
$4.1M
Hypothesis Testing using Phylogenies for the 21st century (equipment supplement)R01GM151683 · NIGMS · TEMPLE UNIV OF THE COMMONWEALTH · PI Spencer V. Muse, ANTON NEKRUTENKO · 2024 to 2026
$1.2M
NHGRI NIH HHS R01 HG009299NIAID NIH HHS U24 AI183870NIGMS NIH HHS R01 GM151683
6 · The paper itself

Abstract

Here we present CAPHEINE, a computational workflow that starts with a set of unaligned pathogen sequences and a reference genome and performs a comprehensive exploratory evolutionary analysis of the input data. CAPHEINE pairs nicely with studies of site-level selection dynamics, gene-level positive selection, and lineage-specific shifts in selective pressure. Our workflow is portable across Mac OS, Windows, and Linux, allowing researchers to focus on results.

Identifiers

PMID41846951
PMCPMC12991155

What OpenQuestion holds

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LicenceCC BY-ND
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.