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Add option for user to provide database location (merged from v2.8 br…

…anch) and update version

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Change bowtie2 version check from error to warning to allow for conda…

… bowtie2 package without version information and update version

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Add identity_threshold option to split nucleotide and translated id o…

…ptions for each allowed_proteins search, resolves additional unclassified genes reported from ids below translated threshold

Update to new utility mapping database file name

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Update version