=== Version 4
* Adoption of the species-level genome bins system (SGBs).
* New MetaPhlAn marker genes extracted identified from ~1M microbial genomes.
* Ability to profile 21,978 known (kSGBs) and 4,992 unknown (uSGBs) microbial species.
* Better representation of, not only the human gut microbiome but also many other animal and ecological environments.
* Estimation of metagenome composed by microbes not included in the database with parameter --unclassified_estimation.
* Compatibility with MetaPhlAn 3 databases with parameter --mpa3

=== Version 3.1
* 433 low-quality species were removed from the MetaPhlAn 3.1 marker database and 2,680 species were added (for a new total of 15,766; a 17% increase).
* Marker genes for a subset of existing bioBakery 3 species were also revised.
* Most existing bioBakery 3 species pangenomes were updated with revised or expanded gene content.
* MetaPhlAn 3.1 software has been updated to work with revised marker database.

=== Version 3.0
* New MetaPhlAn marker genes extracted with a newer version of ChocoPhlAn based on UniRef
* Estimation of metagenome composed by unknown microbes with parameter `--unknown_estimation`
* Automatic retrieval and installation of the latest MetaPhlAn database  with parameter `--index latest`
* Virus profiling with `--add_viruses`
* Calculation of metagenome size for improved estimation of reads mapped to a given clade
* Inclusion of NCBI taxonomy ID in the ouput file
* CAMI (Taxonomic) Profiling Output Format included
* Removal of reads with low MAPQ values

=== Version 2.2.0
- added option "marker_counts" (by Nicola)

=== Version 2.1.0
- added min_alignment_len option to filter out short alignments in local mode. For long reads (>150) it is now recommended to use local mapping together with "--min_alignment_len 100" to filter out very short alignments. (by Tin)
- added "--samout" option to store the mapping file in SAM format (the SAM will be compressed if the extension of the specified output file ends with ".bz2") (by Tin)
- fix: MetaPhlAn2 now ingores about ~300 markers that were a-specific (thanks to Eric)

=== Version 2.0.0
- fix: Biom >= 2.0.0 has the clade IDs second and the sample ids third'
- added extract_markers.py
- fix: #5; revamp biom generation; set clade IDs as enumeration
- added utils/metaphlan2krona.py
