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	1982	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	4866	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	1028	August 4, 2022
calculate_diversity.R script is not working properly	1	40	March 15, 2026
MetaPhlAn removes the database then complains there is no database	0	19	March 12, 2026
Newick tree for mpa_vJan25_CHOCOPhlAnSGB_202503	1	20	March 6, 2026
Metaphlan genus level relative abundance not summing up to 100% and possible database problem	9	905	March 4, 2026
biobakery_workflows 3.1 with MetaPhlAn 3 vs 4 — what are the differences?	0	17	February 24, 2026
Reverse forward reads as input in MetaPhlAn 4	2	40	February 17, 2026
Extending the metaphlan4 database (Jan2025) to include subspecies	2	43	February 13, 2026
Difference in sequencing depth	0	18	February 5, 2026
Metaphlan flags and parameters for extreme metagenomes	1	17	January 30, 2026
Discrepancy between estimated_number_of_reads_from_the_clade and the relative_abundance	0	24	January 20, 2026
SGB identifiers in different versions of Metaphlan database	0	58	December 22, 2025
SGB Newick file labels	2	71	December 16, 2025
Sgb_to_gtdb_profile.py keep read count estimation from -t rel_ab_w_read_stats	9	528	December 12, 2025
Very-sensitive-local preset and unclassified reads in non-human gut samples	0	35	December 11, 2025
Unable to merge virus profile.txt files into table	3	232	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	164	November 20, 2025
RA fixing of vJun23_202307 DB	0	54	November 7, 2025
Metaphlan Results Interpretation	2	93	November 5, 2025
Presence of fungi in ChocoPhlAn vJan25	1	87	October 30, 2025
Metaphlan --install deletes minimap fasta	2	114	October 29, 2025
Allowing bowtie2 memory mapping in metaphlan	3	573	October 28, 2025
Connecting SGB ID with fasta of a MAG/genome?	0	71	October 28, 2025
Rarecurve on long read from Metaphlan 4.2.2	3	85	October 27, 2025
Best practices for visualizing MetaPhlAn 4 MAG identifiers (SGB, FGB, etc.)?	1	77	October 27, 2025
MetaPhlan doesn't detect any microbial samples	2	70	October 27, 2025
ERROR: The Viral Sequence Clusters mode with fasta files requires to specify a SAM output file	1	24	October 27, 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

1982

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

4866

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…