ArticleBioinformatics (Oxford, England)2017
Historian: accurate reconstruction of ancestral sequences and evolutionary rates.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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
17 citing papers in PubMed.
- Deep models of protein evolution in time generate realistic evolutionary trajectories and functional proteins.bioRxiv : the preprint server for biology · 2026Article
- Ancestral reconstruction supports that loss of Nef-mediated T cell modulation coincided with the emergence of pathogenic lentiviruses.Journal of virology · 2025Article
- Algorithms to reconstruct past indels: The deletion-only parsimony problem.PLoS computational biology · 2025Article
- Impact of Phylogenetic Method Choice on Indel Analyses in HIV-1 Subtype B.Genome biology and evolution · 2025Article
- Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction.BMC bioinformatics · 2024Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Ancestral Sequence Reconstruction as a Tool to Detect and Study De Novo Gene Emergence.Genome biology and evolution · 2024Article
- Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.Molecular biology and evolution · 2024Article
- GUANinE v1.0: Benchmark Datasets for Genomic AI Sequence-to-Function Models.bioRxiv : the preprint server for biology · 2024Article
- Ultrafast classical phylogenetic method beats large protein language models on variant effect prediction.Advances in neural information processing systems · 2024Article
- Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses.Molecular biology and evolution · 2023Article
- Machine Boss: rapid prototyping of bioinformatic automata.Bioinformatics (Oxford, England) · 2021Article
- Revisiting Evaluation of Multiple Sequence Alignment Methods.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants?Computational and structural biotechnology journal · 2021Review
- Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations.Genome research · 2019Article
- Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets.Systematic biology · 2019Article
- Solving the master equation for Indels.BMC bioinformatics · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
Motivation: Reconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Results: Historian combines an efficient reimplementation of the ProtPal algorithm with performance-improving heuristics from other alignment tools. Simulation results on fidelity of rate estimation via ancestral reconstruction, along with evaluations on the structurally informed alignment dataset BAliBase 3.0, recommend Historian over other alignment tools for evolutionary applications. Availability and Implementation: Historian is available at https://github.com/evoldoers/historian under the Creative Commons Attribution 3.0 US license. Contact: ihholmes+historian@gmail.com.
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.