HomoloSampler

This is a command line tool for sampling related sequences from Ensembl. It requires PyCogent, Numpy, SQLAlchemy, PyMysql, Click and SciTrack. At present, this tool provides capabilities to support sampling one-to-one orthologs from protein coding genes stored in an Ensembl MySQl database. It can either write out the protein coding sequences from the canonical CDS, or it can write out the Ensembl multiple sequence alignment of the entire gene with annotated features masked.