AMRFinderPlus v3.6.15

The primary update in this release is the way HMM accessions are handled for hits
that are both based on BLAST and HMM hits. It also includes a minor bug fix.

• HMM id and HMM description columns no longer use data from matching node in the hierarchy
• Fix for space in database path issue #23
• Fixed bug where missing DNA sites were not output using --mutation_all

AMRFinderPlus v3.6.10

This is primarily a bug fix release, but some other improvements have been made.

• Fixes issue #21 crash when --mutation_all and -O Escherichia options are used together
• amrfinder will now dereference a soft link to find its run directory
• Additional tests were added for point mutations
• Refactored sequence identifier handling with --pgap option

AMRFinderPlus v3.6.7

This is a bug fix release.

The previous version (3.6.4) failed to run on newer versions of Ubuntu (#20).

AMRFinderPlus no longer prints a cryptic message and dumps core when passed an empty protein FASTA file.

This also includes some code that changes the behavior of the --pgap option where 'gnl|' portions of the sequence identifier are no longer trimmed in the "Contig id" field of the AMRFinderPlus output.

AMRFinderPlus v3.6.4

AMRFinderPlus v3.6.4 includes a significant rewrite of the mutation detection code to enable the detection of small indels and promoter mutations. This has necessitated a change in the database format.

In order to use the latest version of the AMRFinderPlus database (2020-01-06.1 at the time of release) you must upgrade to this version of the software.

Because this version is incompatible with AMRFinderPlus databases from previous versions, amrfinder -u must be run once this update is installed to get the latest version of the database.

AMRFinderPlus v3.2.3

This release contains only small changes from the previous release.

Minor bug fixes:

• bifunctional not included in "Product Name" for BLAST hits to fusion genes
• Minor LANG dependent hit sorting issue
• Improved error messages for missing database_format_version.txt

Modifications to behavior when --gpipe and --organism options are combined for internal NCBI pipeline use.

AMRFinderPlus v3.2.1

AMRFinderPlus v3.2.1 includes several bug fixes and a change to the format and organization of the databases.

In order to use the latest version of the AMRFinderPlus database (2019-10-30.1 at the time of release) you must upgrade to this version of the software.

Because this version is incompatible with AMRFinderPlus databases from previous versions, amrfinder -u must be run once this update is installed to get the latest version of the database.

AMRFinderPlus v3.1.1b

Bug fix release

AMRFinderPlus v3.1.0b

Initial beta release of version 3.1.0 which enables the addition of genes near universal in some taxa that may be functionally informative in others.

AMRFinderPlus v3.0.12

Minor updates mostly for development and internal deployment purposes

AMRFinderPlus v3.0.11

Minor updates to help with bioconda package compilation (PD-2844)