MetaPhlAn

Topic	Replies	Views	Activity
MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update) Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhlAn database (vJan25_…	2	2091	June 11, 2025
Announcing MetaPhlAn 4 MetaPhlAn 4 Release Notes The new MetaPhlAn 4 integrates information from both metagenome assemblies and microbial isolate genomes for improved and more comprehensive metagenomic taxonomic profiling (https://doi.org/10.1…	7	4889	June 8, 2023
Announcing MetaPhlAn 3.1 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 micro…	2	1037	August 4, 2022
Total Bacteria species relative abundance no longer sums to 1 after converting the SGB profile to GTDB	15	1416	April 24, 2026
Matching/linking profiled species using MetaPhlAn3 (v3.0.1) to MetaPhlAn (4.2.4),database: mpa_vJan25_CHOCOPhlAnSGB_202503	0	15	April 9, 2026
Difference in sequencing depth	2	32	April 9, 2026
Metaphlan 3.0.7 related problem with deep sequenced wgs file	0	9	April 3, 2026
Strain taxonomic level Identification	2	115	April 2, 2026
Inquiry regarding qPCR primer design for uncharacterized SGBs using the CHOCOPhlAn marker database	0	12	April 1, 2026
HUMANN3.9 cannot recognize MetaPhlAn 4.2.2 output file	11	493	April 1, 2026
Metaphlan genus level relative abundance not summing up to 100% and possible database problem	10	923	March 23, 2026
calculate_diversity.R script is not working properly	1	51	March 15, 2026
MetaPhlAn removes the database then complains there is no database	0	41	March 12, 2026
Newick tree for mpa_vJan25_CHOCOPhlAnSGB_202503	1	33	March 6, 2026
biobakery_workflows 3.1 with MetaPhlAn 3 vs 4 — what are the differences?	0	21	February 24, 2026
Reverse forward reads as input in MetaPhlAn 4	2	47	February 17, 2026
Extending the metaphlan4 database (Jan2025) to include subspecies	2	57	February 13, 2026
Metaphlan flags and parameters for extreme metagenomes	1	21	January 30, 2026
Discrepancy between estimated_number_of_reads_from_the_clade and the relative_abundance	0	29	January 20, 2026
SGB identifiers in different versions of Metaphlan database	0	65	December 22, 2025
SGB Newick file labels	2	77	December 16, 2025
Sgb_to_gtdb_profile.py keep read count estimation from -t rel_ab_w_read_stats	9	531	December 12, 2025
Very-sensitive-local preset and unclassified reads in non-human gut samples	0	43	December 11, 2025
Unable to merge virus profile.txt files into table	3	233	November 27, 2025
Euks in bt2 index but not in .fna?	0	22	November 24, 2025
Minimap2 Database Files for MetaPhlAn 4.2.2	7	183	November 20, 2025
RA fixing of vJun23_202307 DB	0	61	November 7, 2025
Metaphlan Results Interpretation	2	100	November 5, 2025
Presence of fungi in ChocoPhlAn vJan25	1	98	October 30, 2025
Metaphlan --install deletes minimap fasta	2	129	October 29, 2025

MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update)

Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhlAn database (vJan25_…

2

2091

June 11, 2025

Announcing MetaPhlAn 4

MetaPhlAn 4 Release Notes The new MetaPhlAn 4 integrates information from both metagenome assemblies and microbial isolate genomes for improved and more comprehensive metagenomic taxonomic profiling (https://doi.org/10.1…

7

4889

June 8, 2023

Announcing MetaPhlAn 3.1

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 micro…