v1.0.2

What's New

PrimerCheck

Oligonucleotide analysis and primer design toolkit:

• Analyze — Tm (4 methods), MW, GC%, extinction coefficient, hairpin/self-dimer/hetero-dimer prediction, Tm mismatch heatmaps
• Check — In-silico PCR with mismatch tolerance
• Design — Primer3-powered primer design with full parameter control
• BLAST — NCBI BLAST search for specificity checking

Diversity

Combined alpha and beta diversity analysis:

• Alpha — 10 metrics (Observed Features, Chao1, ACE, Shannon, Simpson, Pielou's Evenness, Inverse Simpson, Berger-Parker, Faith's PD), rarefaction curves, statistical testing (Mann-Whitney, Kruskal-Wallis, Dunn's post-hoc)
• Beta — 7 distance metrics (Bray-Curtis, Jaccard, Canberra, UniFrac, Euclidean, Correlation, Aitchison), 4 ordination methods (PCoA, NMDS, t-SNE, PCA), statistical tests (PERMANOVA, PERMDISP, ANOSIM, pairwise PERMANOVA, Mantel)

SeqConvert

• Added light/dark theme toggle matching other tools

Docker

docker pull eriklysoe/biotools:v1.0.2

v1.0.1

What's New

PhyloTree

• Phylogenetic tree builder with interactive D3.js visualization
• Alignment methods: MUSCLE, ClustalOmega, built-in pairwise
• Tree-building algorithms: Neighbor-Joining, UPGMA, Maximum Likelihood (IQ-TREE)
• Export trees in Newick, Nexus, PhyloXML, and NeXML formats
• Light/dark theme toggle

PCoA (Principal Coordinates Analysis)

• Abundance table parsing (CSV/TSV, auto-detected)
• Distance metrics: Bray-Curtis, Jaccard, Euclidean, Correlation
• Normalisation: None, Total-sum scaling (TSS), Hellinger transformation
• Interactive 2D/3D Plotly.js scatter plots
• Optional metadata colouring and shaping
• Distance matrix display and CSV downloads
• Light/dark theme toggle

Docker Hub

docker run -d -p 5590:5590 eriklysoe/biotools:v1.0.1

v1.0.0

BioTools v1.0.0

Initial release combining two bioinformatics tools into a single self-hosted web app.

Tools

• SeqConvert — Biological sequence format converter (FASTA, GenBank, FASTQ, EMBL, and ~35 more formats) powered by Biopython
• Venn Diagram — Interactive Venn diagram tool for comparing 2–4 ID lists with SVG/PNG/PDF/CSV export

Features

• Single Docker container on port 5590
• Shared navigation bar between tools
• REST API for both tools (/api/convert, /api/compare, /api/formats)
• Optional HTTP Basic Auth
• Reverse proxy support (Pangolin, Cloudflare Tunnel, nginx, Traefik)

Quick Start

docker pull eriklysoe/biotools:v1.0.0

Or use the docker compose file in the docker compose/ folder:

docker compose up -d