ReAlignPro

ReAlignPro is a command-line toolkit for:

• fa2maf: identify orthologous regions via LASTZ reciprocal-best hits, align sequences with MUSCLE, and export MAF/TSV outputs.
• maf2bed: extract target-shared, others-absent positions from a MAF/MAF.GZ and write BED3 intervals.
• tsv2fig: generate PDF sequence-table plots from a conservation-matrix TSV.

Installation

pip

pip install realignpro

Note: fa2maf requires external binaries available in PATH:

• lastz
• muscle
• samtools

conda (recommended)

mamba install -c conda-forge -c bioconda realignpro lastz "muscle=3.8.1551" samtools

Quick start

realignpro --help
realignpro fa2maf --help
realignpro maf2bed --help
realignpro tsv2fig --help

License

GPL-3.0