On 2025-08-11, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #525

Phylogenetics

• mrbayes was updated to 905d00fb5243

Ecoregionalization

• claraguess was updated to 8ac53593cef6
• ecoregion_brt_analysis was updated to dcc059f387b6
• ecoregion_clara_cluster was updated to 893b2b010d4a
• ecoregion_cluster_estimate was updated to 8307fa98be22
• ecoregion_eco_map was updated to 876a70f08281
• ecoregion_geonearestneighbor was updated to e5fc90e44599
• ecoregion_taxa_seeker was updated to cec1f7495897
• indicspecies was updated to 3f4138f610d1

QIIME 2

• qiime2__deblur__denoise_16S was updated to 2572fc0f88f2
• qiime2__deblur__denoise_16S was updated to b883cbea5623

Nanopore

• chopper was updated to 7000f98e1c4b
• nanocomp was updated to d4f671d70a65
• nanofilt was updated to a2c318b04f49

Mapping

• bwameth was updated to b6b87635cf29
• kma was updated to 0e8330535ea0
• minimap2 was updated to 6945cd53bd2d

Proteomics

• openms_idmapper was updated to 138a734e21a1

Convert Formats

• uniprot_rest_interface was updated to 60f7e2a6b9c7

Annotation

• coreprofiler_allele_calling was updated to 8b8c1c9c0413
• evidencemodeler was updated to 82aeab1ae0a1
• funannotate_annotate was updated to 0b8d49d3742d
• sortmerna was updated to 10b84b577117

Assembly

• canu was updated to e05f5ee0ffb9
• pairtools_dedup was updated to 608ea80cccba
• pairtools_parse was updated to 729197476fc1
• pairtools_sort was updated to c1c1d894dd3a
• pairtools_split was updated to 0fb51c6f2e37
• pairtools_stats was updated to cfeb5205eacc

None

• amrfinderplus_data_manager_build was updated to eea0c38a9afd
• data_manager_build_bracken_database was updated to 5c8a23ccb14a
• data_manager_build_coreprofiler was updated to c3553950db1b
• data_manager_build_kraken2_database was updated to 9002633b4737
• data_manager_diamond_database_builder was updated to 4a08b7b76b78
• data_manager_humann2_database_downloader was updated to ff9cf22838d4
• data_manager_humann_database_downloader was updated to fea85c467896
• data_manager_semibin was updated to d584aacd7d13

Evolution

• map_damage was updated to 0287e2f82b64
• tn93 was updated to 00a8c36fc98c
• tn93_cluster was updated to 476189b83931
• tn93_filter was updated to 017db1b776d9
• tn93_readreduce was updated to 4e68161336da

FASTA/FASTQ

• cialign was updated to 3c5bdab3c7b7

Filter and Sort

• gffcompare was updated to a3e78550e42e

Get Data

• ncbi_datasets was updated to 03a801ded645
• ncbi_datasets was updated to 0f3b3813b6ae
• ncbi_datasets was updated to 95be88b49f4e

HiCExplorer

• schicexplorer_schicadjustmatrix was updated to 658ae96f53c4
• schicexplorer_schiccluster was updated to 3728380d1dff
• schicexplorer_schicclustercompartments was updated to 97569c103d58
• schicexplorer_schicclusterminhash was updated to 74e28c7ca918
• schicexplorer_schicclustersvl was updated to e327fe59be69
• schicexplorer_schicconsensusmatrices was updated to 38ece0c4e316
• schicexplorer_schiccorrectmatrices was updated to f2d2d650f7b5
• schicexplorer_schiccreatebulkmatrix was updated to 14e19124511c
• schicexplorer_schicdemultiplex was updated to a49faacc7c1f
• schicexplorer_schicinfo was updated to b3b17288df08
• schicexplorer_schicmergematrixbins was updated to 48ed2580b39e
• schicexplorer_schicmergetoscool was updated to d92e3bca3da0
• schicexplorer_schicnormalize was updated to 12825fd4c91c
• schicexplorer_schicplotclusterprofiles was updated to 0aca9bf1e402
• schicexplorer_schicplotconsensusmatrices was updated to b1f0a9b02efd
• schicexplorer_schicqualitycontrol was updated to e426ba8aeb93

Metagenomic Analysis

• comebin was updated to 15f6ef1d7c96
• comebin was updated to 5910c5106cdc
• krakentools_alpha_diversity was updated to 7337f9722ad7
• krakentools_beta_diversity was updated to 5fa703b1f68a
• krakentools_combine_kreports was updated to 59fa9d9f4e34
• krakentools_extract_kraken_reads was updated to 3b1963f729cb
• krakentools_kreport2krona was updated to 05e78a90e02d
• krakentools_kreport2mpa was updated to fd7d3bfb0fa8
• last was updated to cb132bfc5ab1
• micro_decon was updated to bd267e082f86
• pimento_are_there_primers was updated to 7a97ac708fee
• pimento_auto was updated to f41d29b1a43e
• pimento_choose_primer_cutoff was updated to 16d91d782bf8
• pimento_find_cutoffs was updated to eba53f3623c9
• pimento_gen_bcv was updated to 790332d37eb1
• pimento_std was updated to 1ddab994fcee
• semibin was updated to bcb50c148f4b
• semibin_bin was updated to 552cfc6ed475
• semibin_concatenate_fasta was updated to c72b50829c03
• semibin_generate_cannot_links was updated to 416bfa61b640
• semibin_generate_sequence_features was updated to 40ffba87bbcf
• semibin_train was updated to 191a3a14a7f1
• virannot_blast2tsv was updated to 5c53a5baaf72
• virannot_otu was updated to b98e11966036
• virannot_rps2tsv was updated to aac02a3a395c

NCBI Blast

• diamond was updated to 8b8a3f793f0f

RNA Analysis

• htseq_count was updated to 8f6836089479

SAM/BAM

• mosdepth was updated to b1a8d09e5a82

Send Data

• ena_webin_cli was updated to c9f87770ba8f

Statistics

• fastspar was updated to e9231fb122e9

Variant Calling

• freebayes was updated to 0d8581534009
• lofreq_filter was updated to 950d1d49d678

Virology

• freyja_aggregate_plot was updated to 3d9253661554
• freyja_boot was updated to 2d1bfff73837
• freyja_demix was updated to e9f497a660d6
• freyja_variants was updated to eccec0876e54
• ivar_consensus was updated to 1c5448133894
• ivar_filtervariants was updated to 161e04f498db
• ivar_variants was updated to 5e5dfc9e71e2

Imaging

• gate_finder was updated to 64609b94f90f
• vitessce_spatial was updated to cab38f254824