# Announcing MetaPhlAn 3.1 and HUMAnN 3.1 **URL:** \ **Category:** HUMAnN\ **Created:** [July 27, 2022, 6:20pm UTC](https://forum.biobakery.org/t/announcing-metaphlan-3-1-and-humann-3-1/3881 "2022-07-27T18:20:08Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [July 27, 2022, 6:20pm UTC](https://forum.biobakery.org/t/announcing-metaphlan-3-1-and-humann-3-1/3881/1 "2022-07-27T18:20:08Z")
# MetaPhlAn 3.1 / HUMAnN 3.1 Release Notes MetaPhlAn 3.1 and HUMAnN 3.1 represent a moderate update to the bioBakery 3 software and databases. This update is based on improvements in our ability to align NCBI-sourced microbial genomes and their constituent genes to UniProt resources alongside removal of additional low-quality species (see [PMID:33944776](https://pubmed.ncbi.nlm.nih.gov/33944776/) for the definition of “low-quality species”). ## What has changed in v3.1: - MetaPhlAn 3.1: 2,680 species were added to the marker database and 433 low-quality species were removed (new total = 15,766: a 17% increase). - MetaPhlAn 3.1: Marker genes for a minority subset of existing bioBakery 3 species were also revised. - HUMAnN 3.1: 2,132 species were added to the pangenome database and 645 low-quality species were removed (new total = 12,773: a 13% increase). - HUMAnN 3.1: Pangenomes of most existing bioBakery 3 species were updated with revised or expanded gene content. - Minor software updates. ## What has NOT changed in v3.1: - UniProt-derived resources included with bioBakery 3 (e.g. the DIAMOND-formatted UniRef90/50 databases) have not changed and do not need to be updated. - MetaPhlAn 3.1 and HUMAnN 3.1 remain focused on microbial isolate genomes sourced from NCBI. See the section [“What’s next for bioBakery?”](#whats-next-for-biobakery) at the end of this document for updates on profiling species defined or expanded from metagenome-assembled genomes (MAGs). ## How to perform a fresh install of MetaPhlAn 3.1 and HUMAnN 3.1: - See here for instructions on installing MetaPhlAn 3.1 in a new environment: - See here for instructions on installing HUMAnN 3.1 in a new environment: ## How to upgrade from earlier versions of MetaPhlAn 3 and HUMAnN 3: - Update HUMAnN with `pip`: - Download the new MetaPhlAn 3.1 marker database: - Download the new HUMAnN 3.1 pangenome database (`full_chocophlan.v201901_v31.tar.gz`) to a NEW folder: - You DO NOT need to re-download the HUMAnN 3.1 DIAMOND-formatted UniRef90/50 databases or the accessory mapping files. ## What’s next for bioBakery? - The next generation of MetaPhlAn (v4) will support profiling the abundances of species genome bins (SGBs) as derived from a combination of isolate genomes and metagenome-assembled genomes in [PMID:30661755](https://pubmed.ncbi.nlm.nih.gov/30661755/). - MetaPhlAn v4 will be released soon alongside an update to HUMAnN (v3.5) that will enable users to combine SGB-based taxonomic profiles with the current (v3.1) pangenomes. - HUMAnN v4 (enabling functional profiling from SGBs) is also in development, but will release later. ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [July 27, 2022, 6:21pm UTC](https://forum.biobakery.org/t/announcing-metaphlan-3-1-and-humann-3-1/3881/2 "2022-07-27T18:21:04Z")
Pinned on July 27, 2022, 6:21pm UTC ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [October 4, 2022, 1:33pm UTC](https://forum.biobakery.org/t/announcing-metaphlan-3-1-and-humann-3-1/3881/3 "2022-10-04T13:33:43Z")
Unpinned on October 4, 2022, 1:33pm UTC