ArticleJournal of molecular evolution2025
OrthoGrafter: Rapid Identification of Orthologs from Precomputed Placement in Phylogenetic Trees.
Article in Journal of molecular evolution, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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.
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.
Who cites it
1 citing paper in PubMed.
- Perspectives on Orthology During the Quest for Orthologs.Journal of molecular evolution · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The identification of orthologs plays an important role in comparative genomics and function inference. Here, we present OrthoGrafter, a bioinformatics tool for taking one or more query sequences and inferring a set of orthologs drawn from the collection of 143 well annotated species in the PANTHER database of reconciled gene trees. OrthoGrafter takes sets of graft points output by the highly used TreeGrafter software (either the standalone package or InterProScan), and for each one, outputs a list of predicted orthologous genes from the grafted PANTHER tree (with the ability to additionally output paralog and xenolog sets). If the taxonomic identifier for the query is also provided, OrthoGrafter incorporates the novel step of adjusting the graft point to facilitate consistent taxonomic assignment for the graft within the reconciled gene family, which we demonstrate shows an improvement in the ortholog inference via correlation with orthologs provided by the OMA database. Lightweight and utilizing precomputed results to enable rapid determination of ortholog predictions for large sample groups, OrthoGrafter is available at https://github.com/pantherdb/OrthoGrafter. .
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.