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PROTÉGÉ PD

Design phylogenetic primers from protein-coding gene sequences with intelligent degeneracy analysis and interactive visualization

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Quick start

Get PROTÉGÉ PD running in three simple steps

1

Install Docker

PROTÉGÉ PD runs in a Docker container. Install Docker Desktop for your operating system:
2

Pull the Docker image

Download the PROTÉGÉ PD Docker image from Docker Hub:
docker pull ddelgadillo/protege_base:v1.0.2
3

Run PROTÉGÉ PD

Launch the container with your FASTA file. Replace /your/files/path/ with your data directory and myseqs.fna with your file name:
docker run --rm \
  --mount type=bind,source=/your/files/path/,target=/root/. \
  --name protege \
  -p 127.0.0.1:8050:8050 \
  --cpus 4 \
  ddelgadillo/protege_base:v1.0.2 \
  protege-pd -s myseqs.fna
The web interface will launch at http://127.0.0.1:8050
When PROTÉGÉ PD starts successfully, you’ll see:
  • Sequence translation and alignment progress
  • Consensus calculation for each position
  • Web server startup message
  • Access URL: http://127.0.0.1:8050

Explore by topic

Learn about PROTÉGÉ PD’s capabilities and workflows

PhyloTag approach

Understand the phylogenetic tag methodology for primer design

Command reference

Complete guide to all CLI options and parameters

Primer degeneracy

Learn how PROTÉGÉ PD calculates and optimizes primer degeneracies

Web interface

Interactive visualization and primer selection

Sequence alignment

MUSCLE alignment and consensus sequence calculation

Melting temperature

Multiple Tm calculation methods for primer validation

Key features

Everything you need for phylogenetic primer design

Multiple sequence alignment

Automated MUSCLE alignment of protein-coding sequences for accurate consensus generation

Degeneracy analysis

Intelligent calculation of primer degeneracies with configurable consensus thresholds

Interactive visualization

Web-based Dash interface for exploring primer positions and melting temperatures

Melting temperature methods

Four calculation methods including Wallace, GC-based, and nearest-neighbor thermodynamics

Ready to design phylogenetic primers?

Get started with PROTÉGÉ PD and streamline your primer design workflow with automated alignment, degeneracy analysis, and interactive visualization.

Install PROTÉGÉ PD