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	2170	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	4900	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	1041	August 4, 2022
Correupt bowtie2 index file? metaphlan error	0	9	May 13, 2026
Nanopore long-reads analysis with Metaphlan4.2.2	0	3	May 12, 2026
Beta diversity in metaphlan 4.2.4 doesn't work becuase of rbiom upgrade?	0	6	May 11, 2026
mpa_vJan25_CHOCOPhlAnSGB_202503.fna not downloaded in the .tar file	2	32	May 11, 2026
Total Bacteria species relative abundance no longer sums to 1 after converting the SGB profile to GTDB	16	1431	May 6, 2026
Matching/linking profiled species using MetaPhlAn3 (v3.0.1) to MetaPhlAn (4.2.4),database: mpa_vJan25_CHOCOPhlAnSGB_202503	0	20	April 9, 2026
Difference in sequencing depth	2	38	April 9, 2026
Metaphlan 3.0.7 related problem with deep sequenced wgs file	0	13	April 3, 2026
Strain taxonomic level Identification	2	124	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	513	April 1, 2026
Metaphlan genus level relative abundance not summing up to 100% and possible database problem	10	925	March 23, 2026
calculate_diversity.R script is not working properly	1	55	March 15, 2026
MetaPhlAn removes the database then complains there is no database	0	58	March 12, 2026
Newick tree for mpa_vJan25_CHOCOPhlAnSGB_202503	1	38	March 6, 2026
biobakery_workflows 3.1 with MetaPhlAn 3 vs 4 — what are the differences?	0	22	February 24, 2026
Reverse forward reads as input in MetaPhlAn 4	2	51	February 17, 2026
Extending the metaphlan4 database (Jan2025) to include subspecies	2	67	February 13, 2026
Metaphlan flags and parameters for extreme metagenomes	1	23	January 30, 2026
Discrepancy between estimated_number_of_reads_from_the_clade and the relative_abundance	0	30	January 20, 2026
SGB identifiers in different versions of Metaphlan database	0	70	December 22, 2025
SGB Newick file labels	2	79	December 16, 2025
Sgb_to_gtdb_profile.py keep read count estimation from -t rel_ab_w_read_stats	9	532	December 12, 2025
Very-sensitive-local preset and unclassified reads in non-human gut samples	0	46	December 11, 2025
Unable to merge virus profile.txt files into table	3	239	November 27, 2025
Euks in bt2 index but not in .fna?	0	24	November 24, 2025
Minimap2 Database Files for MetaPhlAn 4.2.2	7	198	November 20, 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

2170

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

4900

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…