ArticleBriefings in bioinformatics2011
PHAST and RPHAST: phylogenetic analysis with space/time models.
Article in Briefings in bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 358 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
358 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).Genetics in medicine : official journal of the American College of Medical Genetics · 2022Guideline
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.Genome biology · 2026Article
- Horizontal gene transfer rivals gene duplication as a source of anti-parasitoid immune innovation in the Drosophilidae.bioRxiv : the preprint server for biology · 2026Article
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- Functional convergence of regulatory regions provides vital insights into mammalian gliding adaptation.Science China. Life sciences · 2026Article
- Comparative analysis of conserved non-coding elements identifies gene regulatory networks rewired during the water-to-land transition in vertebrates.Biologia futura · 2026Article
- Disruption of mitonuclear coadaptation and compensatory evolution after an extreme dietary shift in carnivorous butterflies.Molecular biology and evolution · 2026Article
- Article
- Pig Matrix: a matched multiomics 3D regulatory genomics database for evolutionary and comparative analyses in pigs.Molecular biology and evolution · 2026Article
- Unveiling New Insights: ReinterpretingClinical case reports · 2026Article
- CNEwrap: a scalable toolkit with a novel algorithm for large-scale genome-wide accelerated conserved non-coding elements detection.Nucleic acids research · 2026Article
- SNPnexus: an enhanced web platform for large-scale and multi-sample variant analysis (2025 update).Nucleic acids research · 2026Article
- The origin and evolution of dorsal determination mechanisms in vertebrate paired appendages.Current biology : CB · 2026Article
- Genomic insights into marine-freshwater transition: evolutionary adaptations in freshwater Pusa seals.Genetica · 2026Article
- Phylogenomic blind spots: the limits of UCE and BUSCO loci in the presence of gene flow.Molecular biology and evolution · 2026Article
- circASbase: A Comprehensive Database of Alternative Splicing Events in circRNAs.Genomics, proteomics & bioinformatics · 2026Article
- Genetic Heterogeneity of Autism Spectrum Disorder: Identification of Five Novel Mutations (RIMS2, FOXG1, AUTS2, ZCCHC17, and SPTBN5) in Iranian Families via Whole-Exome and Whole-Genome Sequencing.Biochemical genetics · 2026Article
- Lift&Add-rapid and robust addition of new species to alignments of conserved non-coding sequences.Bioinformatics (Oxford, England) · 2026Article
- Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation.bioRxiv : the preprint server for biology · 2026Article
- Comparative genomics reveals LINE-1 recombination with diverse RNAs.Cell genomics · 2026Article
298 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
3 authors.
Funding
Abstract
The PHylogenetic Analysis with Space/Time models (PHAST) software package consists of a collection of command-line programs and supporting libraries for comparative genomics. PHAST is best known as the engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser. However, it also includes several other tools for phylogenetic modeling and functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations. PHAST has been in development since 2002 and has now been downloaded more than 1000 times, but so far it has been released only as provisional ('beta') software. Here, we describe the first official release (v1.0) of PHAST, with improved stability, portability and documentation and several new features. We outline the components of the package and detail recent improvements. In addition, we introduce a new interface to the PHAST libraries from the R statistical computing environment, called RPHAST, and illustrate its use in a series of vignettes. We demonstrate that RPHAST can be particularly useful in applications involving both large-scale phylogenomics and complex statistical analyses. The R interface also makes the PHAST libraries acccessible to non-C programmers, and is useful for rapid prototyping. PHAST v1.0 and RPHAST v1.0 are available for download at http://compgen.bscb.cornell.edu/phast, under the terms of an unrestrictive BSD-style license. RPHAST can also be obtained from the Comprehensive R Archive Network (CRAN; http://cran.r-project.org).
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.