Overview

camlhmp provides a set of command line interface (CLI) commands for typing organisms. These commands are designed to be easy to use and provide a simple way to type organisms using the available engines and schemas.

Currently the following commands are available in the camlhmp CLI:

Command	Description
camlhmp-blast-alleles	Classify assemblies using BLAST against alleles of a set of genes
camlhmp-blast-regions	Classify assemblies using BLAST against larger genomic regions
camlhmp-blast-targets	Classify assemblies using BLAST against individual genes or proteins
camlhmp-extract	Extract typing targets from a set of reference sequences