picotainers/muscle repository overview

⁠muscle

⁠how to run

⁠MUSCLE - Multiple Sequence Comparison by Log-Expectation

A containerized implementation of MUSCLE, a powerful multiple sequence alignment tool used in bioinformatics for aligning protein and DNA sequences.

⁠Overview

MUSCLE is an efficient and accurate tool for creating multiple alignments of amino acid or nucleotide sequences. This Docker image provides a lightweight, portable solution for sequence alignment workflows, ideal for both standalone use and integration into bioinformatics pipelines.

⁠Quick Start

Basic alignment:

docker run --platform linux/amd64 -it --rm -v "$(pwd):/data" picotainers/muscle --align /data/query.fasta --output /data/query.aln

⁠Parameters

• --align: Input FASTA file containing sequences to align
• --output: Output file path for the alignment results

⁠Volume Mounting

Use -v "$(pwd):/data" to mount your current directory, allowing the container to access your sequence files.

⁠Requirements

• Docker installed
• Input sequences in FASTA format
• Sufficient disk space for output alignment files

⁠Use Cases

• Comparative genomics
• Phylogenetic analysis preparation
• Protein structure prediction pre-processing
• Multiple sequence alignment for conservation studies``` docker run --platform linux/amd64 -it --rm -v "$(pwd):/data" picotainers/muscle --align /data/query.fasta --output /data/query.aln