1.4.3

fix setup

1.4.2

update init

1.4.1

update help __main__

Release 1.4

Adding mantis to conda

Release 1.3.1

Fixed a bug in _weight parsing.
Also fixed some other minor issues and updated the wiki

Release 1.3

This is a cumulative release of all the features added since 1.2:

• removed TIGRfams HMMs, since these are included in the NCBI protein family HMMs
• added gff output
• changed NOG reference from HMM to Diamond
• added the option to use GTDB lineages and taxa strings when input organism details (previously it was only NCBI IDs)
• added lowest common ancestor to convert between GTDB and NCBI
• metadata is now converted to SQL which increases efficiency at which we retrieve metadata (this is especially useful for very large metadata files)
• changed config file
• removed NOG sql files
• added check_sql option to check if SQL databases are working correctly
• Removed slurm variables (now Mantis will use all available cores instead of the ones given by slurm, the user should therefore set the amount of cores to be used)

1.2.3

Added gff output

Removed tigrfams default HMM

TIGRFAMs is no longer directly available from NCBI, instead it is now part of their broader protein family HMMs, which are already part of the Mantis' default HMMs.
TIGRfams was therefore removed.

NCBI now also contains go terms, so these were added to the respective metadata.

1.2

This is a cumulative release, it includes all previous features, i.e., km improvement and diamond support, as well as the bug fixes.
A different folder structure for some default databases was also previously included.

This release uses a different structure for custom references, therefore it will break previous metadata files for custom references.
Keep in mind that this is only applicable to custom references, default references are not affected.

km improvement

changed km to actually represent kegg matrix completeness; added verb…

…ose mode

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