MISPhyl: Mutual Information Supermatrix Phylogenomics pipeline

Classification of species, particularly pathogens are important in understanding mode of infections, their origins and even treatments. The advancement of sequencing technologies has offered a parallel advancement in species classification with the used of phylogenomics. The success of phylogenomics requires a series of bioinformatics methods and procedures, which would be a challenge for most clinical analysts or researchers. Herein, we present MISPhyl (Mutual Information Supermatrix Phylogenomics), an automated pipeline developed to facilitate the reconstruction of high confidence supermatrix tree using the median-ranked single-copy core orthologous genes (SCGs) evaluated via mutual information in annotated genome sets. In house accessory scripts for sequence quality assessments, renaming FASTA headers and subsampling based on mutual information are distributed along with MISPhyl, made publicly available (https://github.com/pendy05/MISPhyl)