ArticleNucleic acids research2015
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 380 papers, 1 of them a synthesis that pooled 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.
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
380 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Detailed Systematic Review on Retinal Image Segmentation Methods.Journal of digital imaging · 2022Pooled it
- Distinct Evolutionary Trajectories of Major Intracellular Proteolytic Systems in Gilthead Seabream and European Seabass.Biology · 2026Article
- Optimal Partitioning for Molecular Phylogenetic Inference and Generic Delimitation in the Cetrarioid Core Group (Parmeliaceae, Ascomycota).Journal of fungi (Basel, Switzerland) · 2026Article
- Transcription Factor Evolution Associated with Social Transitions in Blattodea.Journal of molecular evolution · 2026Article
- Replication-transcription collisions impose DNA strand-specific constraints on gene length in bacteria.PLoS genetics · 2026Article
- A deep learning-based score to evaluate multiple sequence alignments.Molecular biology and evolution · 2026Article
- Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models.Molecular biology and evolution · 2026Article
- Taxonomy and Phylogeny of Two NewAnimals : an open access journal from MDPI · 2026Article
- Molecular characterization of Sarcocystis spp. in intestines of coyotes and foxes from Pennsylvania, USA.Parasites & vectors · 2026Article
- Thermodynamic variations at the HPV E1-E2 interface correlate with clinical risk groups: an in-silico analysis.Virology journal · 2026Article
- Deciphering APOBEC1 in Avians: unravelling loss events and functional insights.Immunogenetics · 2026Article
- The evolutionary dynamics between viral mimics and host proteins.Molecular systems biology · 2026Article
- Unveiling the carbohydrate-active enzyme repertoire of Trichoderma caribbaeum IHBT through whole-genome analysis and transcriptional profiling.Archives of microbiology · 2026Article
- Strategic Computational Design of siRNA Molecules Targeting Structural Genes of SARS-CoV-2.Applied biochemistry and biotechnology · 2026Article
- Adaptive evolution of odorant receptors is associated with elaborations of social organization in ants.Molecular biology and evolution · 2026Article
- Molecular screening of tick-borne pathogens in host-seeking Haemaphysalis punctata Canestrini & Fanzago, 1878 (Ixodoidea: Ixodidae) in Anatolia with the first report of Burana virus.Parasites & vectors · 2026Article
- Detection of Anaplasma phagocytophilum and Babesia aktasi in a wild bezoar goat (Capra aegagrus): Overlap with domestic goat strains.Medical and veterinary entomology · 2026Article
- Chromosomal rearrangements and segmental deletions contribute to gene loss in squamates.BMC biology · 2026Article
- Article
- Exploring cooperation among social pathogens: a computational perspective.FEMS microbiology reviews · 2026Review
320 more citing papers are in PubMed but not listed here.
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
Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il.
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.