ArticleGenome biology and evolution2014
Indel reliability in indel-based phylogenetic inference.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Evaluation of various distance computation methods for construction of haplotype-based phylogenies from large MLST datasets.Molecular phylogenetics and evolution · 2022Article
- Tatajuba: exploring the distribution of homopolymer tracts.NAR genomics and bioinformatics · 2022Article
- Molecular Phylogeny ofPlants (Basel, Switzerland) · 2021Article
- Article
- Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning.Systematic biology · 2020Article
- Identification and optimization of PrsA in Bacillus subtilis for improved yield of amylase.Microbial cell factories · 2019Article
- Article
- Inferring phylogenetic trees from the knowledge of rare evolutionary events.Journal of mathematical biology · 2018Article
- Split-inducing indels in phylogenomic analysis.Algorithms for molecular biology : AMB · 2018Article
- Article
- SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm.Nucleic acids research · 2017Article
- The nuclear 28S gene fragment D3 as species marker in oribatid mites (Acari, Oribatida) from German peatlands.Experimental & applied acarology · 2017Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is often assumed that it is unlikely that the same insertion or deletion (indel) event occurred at the same position in two independent evolutionary lineages, and thus, indel-based inference of phylogeny should be less subject to homoplasy compared with standard inference which is based on substitution events. Indeed, indels were successfully used to solve debated evolutionary relationships among various taxonomical groups. However, indels are never directly observed but rather inferred from the alignment and thus indel-based inference may be sensitive to alignment errors. It is hypothesized that phylogenetic reconstruction would be more accurate if it relied only on a subset of reliable indels instead of the entire indel data. Here, we developed a method to quantify the reliability of indel characters by measuring how often they appear in a set of alternative multiple sequence alignments. Our approach is based on the assumption that indels that are consistently present in most alternative alignments are more reliable compared with indels that appear only in a small subset of these alignments. Using simulated and empirical data, we studied the impact of filtering and weighting indels by their reliability scores on the accuracy of indel-based phylogenetic reconstruction. The new method is available as a web-server at http://guidance.tau.ac.il/RELINDEL/.
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.