MitoPhAST¶
Description¶
The increased rate at which complete mitogenomes are being sequenced and their increasing use for phylogenetic studies have resulted in a bioinformatics bottleneck in preparing and utilising such data for phylogenetic data analysis. We present, MitoPhAST, an automated tool that: 1) Identifies annotated protein-coding gene (PCG) and ribosomal RNA (rRNA) features directly from complete/partial GenBank/EMBL-format mitogenome files and generates a standardized, concatenated and partitioned nucleotide/amino acid alignments. 1) Incorporates nuclear gene sequences (if supplied by user) into phylogenetic analysis. 2) Generates a maximum likelihood phylogenetic tree using optimized substitution models performed by IQ-TREE. 3) Reports various mitochondrial genes and sequence information in a simple table format. 4) Extracts mitochondrial gene order (MGO) from GenBank files and clusters identical MGOs into groups
Environment Modules¶
Run module spider mitophast to find out what environment modules are available for this application.
Environment Variables¶
- HPC_MITOPHAST_DIR - installation directory
- HPC_MITOPHAST_BIN - executable directory
- HPC_MITOPHAST_DOC - documentation directory
- HPC_MITOPHAST_DAT - data directory
- HPC_MITOPHAST_DB - database directory
Categories¶
phylogenetics