Feature Frequency Profile (FFP) Method: A Language Model for Whole-Genome ("Organism") Phylogeny.

JaeJin Choi, Byung-Ju Kim, Sung-Hou Kim

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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1 · What the graph read from it

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4 · The record

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5 · Who and what money

Authors and funding

3 authors.

JaeJin ChoiDepartment of Chemistry and Center for Computational Biology, University of California, Berkeley, CA, USA.

Byung-Ju KimDepartment of Chemistry and Center for Computational Biology, University of California, Berkeley, CA, USA.

Sung-Hou KimDepartment of Chemistry and Center for Computational Biology, University of California, Berkeley, CA, USA. sunghou@berkeley.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

For almost half a century, molecular phylogenetic methods (based on genomic sequence variations among a small number of genes/proteins that are highly homologous among the study population) have dominated in inferring the evolution of diverse organisms despite many important intrinsic limitations. Strictly speaking, these molecular trees represent the inferred evolution of those molecules selected, neither of organisms, nor of whole genomes (as simplified yet quantifiable proxy for the organism) selected. This is primarily because of two reasons: (a) the technology of economic sequencing and assembling the whole genome of an organism did not emerge until recently, especially for eukaryotic whole genomes, and (b) computational methods of comparing whole-genome sequences efficiently did not emerge until recently due to the sparsity of available whole-genome sequences. An example of a whole-genome Tree of Life is presented.

Indexed as

Computational BiologyGenomeGenomicsPhylogenyAnimalsEvolution, MolecularModels, GeneticFeature frequency profile (FFP)Jensen–Shannon divergenceMolecular treeOrganism treePan-genomic Tree-of-Life (ToL)Rooting of ToLWhole-genome tree

Identifiers

PMID42056696

DOI10.1093/nar/gkab301

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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.