CRESSENT
CRESSENT (CRESS DNA Virus Analysis Tool) is a comprehensive bioinformatics pipeline designed for the analysis of ssDNA viruses. It provides state-of-the-art tools for phylogenetic analysis, recombination detection, motif discovery, and functional annotation of CRESS DNA viruses.
Comprehensive Analysis
CRESSENT integrates multiple analysis modules from sequence preprocessing to advanced phylogenetic comparisons.
Phylogenetic Tools
Build publication-ready phylogenetic trees with integrated alignment visualization and domain-specific analysis.
Motif Discovery
Discover and visualize conserved motifs using both known patterns and de novo discovery methods.
Get started
To start using CRESSENT, read the installation and quickstart guides below. To learn more about specific analysis modules, visit the module pages listed in the sidebar.
Instructions on how to install CRESSENT and its dependencies.
Learn how to run CRESSENT and interpret its results with a step-by-step tutorial.
Analysis Modules
CRESSENT provides a modular analysis framework that can be customized for different research needs:
Quality control, dereplication, decontamination, and sequence adjustment tools.
A module to aligmen your sequences with a custom database.
Sequence alignment, tree building, and comparative phylogenetic analysis.
Pattern-based searching and de novo motif discovery with functional annotation.
Stem-loop and iteron identification for viral replication elements.
Comprehensive recombination analysis using multiple detection methods.
Publication-ready figures including sequence logos, trees, and motif maps.
Pipeline Overview
CRESSENT workflows are designed to be modular and flexible, allowing researchers to combine different analysis modules based on their specific research questions:
Basic Workflow
Data Preprocessing - Quality control and sequence preparation
Motif Analysis - Pattern discovery and functional annotation
Structural Analysis - Secondary structure detection
Phylogenetic Analysis - Evolutionary relationships
Visualization - Publication-ready figures
Advanced Workflows
Comparative Genomics - Multi-genome analysis with recombination detection
Evolutionary Analysis - Deep phylogenetic analysis with tanglegrams
Functional Annotation - Comprehensive motif and domain analysis
Key Features
Comprehensive Analysis Pipeline
Multi-format support for FASTA, GFF, and various annotation formats
Scalable processing from single genomes to large datasets
Quality control with contamination detection and sequence validation
Reproducible workflows with detailed logging and parameter tracking
Advanced Motif Analysis
Pattern-based search using regex with seqkit integration
De novo discovery using MEME for unknown motifs
Functional annotation via ScanProsite database queries
Visualization through information-rich sequence logos
Structural Biology Tools
Stem-loop detection using ViennaRNA folding algorithms
Iteron identification with CRUISE for replication origins
Family-specific analysis for major CRESS virus groups
Validation scoring based on structural and sequence features
Phylogenetic Capabilities
Multiple alignment with MAFFT and trimming with TrimAl
Tree building using IQ-TREE with ModelFinder
Advanced visualization with metadata integration
Comparative analysis through tanglegrams and distance matrices
Publication-Ready Outputs
High-quality figures in multiple formats (PDF, PNG, SVG)
Customizable layouts for different publication requirements
Integrated legends and annotation systems
Scalable graphics for presentations and manuscripts
Citing CRESSENT
If you use CRESSENT in your work, please consider citing:
CRESSENT: a Bioinformatic Toolkit to Explore and Improve ssDNA Virus Annotation
Pavan, R.R., Sullivan, M.B. and Tisza, M., 2025 — Biorxiv, 2025.
DOI: 10.1101/2025.07.14.664782.
Ask a question or report a bug
If you want to ask a question about CRESSENT or report a problem, please create an issue in the GitHub repository.