Software and Tools
The Cohn Lab shares code, tools, and technical resources that support our research and related bioinformatics workflows.
Bioinformatics Web Tools
DIVEIN
- Performs automated maximum-likelihood phylogenetic analyses on aligned sequences, building trees, reconstructing consensus/MRCA/center-of-tree sequences, and computing diversity, divergence, and informative-site statistics to study viral sequence evolution.
Koalafy
- A web-based phylogenetic tree visualization tool designed to automatically identify and stack clonal sequences, with additional annotation capabilities.
IntegrationSites
- Performs a BLAST search against the human genome to detect HIV integration sites, with fallback to a BLAST search against the HIV HXB2 reference sequence if no genomic match is found.
MethylationStation
- Analyzes and visualizes DNA methylation from bisulfite-converted FASTA alignments, mapping CpG site methylation levels per sequence and generating grouped heatmaps and exportable diagrams and summaries.
NGSQC
- Performs quality control of next-generation sequencing data by combining FastQC read-quality metrics, BWA/Minimap2 alignment to a reference (default HXB2), SAMtools mapping statistics, and MultiQC visualization into a single user-friendly report.
QUALITY
- Quantifies target molecules from PCR-based dilution data using a modified minimum chi-squared (χ2) method for limiting dilution assays.
ViroBLAST
- Provides sequence comparison and contamination checking for viral research, allowing users to run nucleotide or amino acid similarity searches against public, local, or user-uploaded sequence databases with organized, easy-to-navigate results.
WebPSSM
- Predicts HIV-1 coreceptor usage (X4 vs. R5) by scoring nucleotide or amino acid sequences of the envelope V3 loop against subtype-specific position-specific scoring matrices.
Technical Support
Questions or feedback about the lab’s technical resources can be sent to cohnlabsupport@fredhutch.org