On 2025-06-16, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #518

Climate Analysis

• tool_biogeochemical_calibration was updated to e10d47d0f447
• tool_odv was updated to 197286c1fcce
• tool_odv_history was updated to 6c6ce67252bc

Machine Learning

• sklearn_generalized_linear was updated to 6cf4b82c72bc
• sklearn_sample_generator was updated to 7c2e71e4acf3

Metabolomics

• isolib was updated to f0fe957df1cc
• matchms_convert was updated to 4845979fbe02

Metagenomic Analysis

• merge_metaphlan_tables was updated to 05ad7d35ce92
• genomad_end_to_end was updated to 26f5822743aa

Data Managers

• genomad_build_database was updated to 34b729713d0c

Imaging

• cp_common was updated to 27396311a314
• doclayoutyolo was updated to 28b4dc80d58b
• json2yolosegment was updated to fa068d13e781
• yolo_predict was updated to af3eed1f1abe
• yolo_training was updated to 92d5c5e5c734
• omero_filter was updated to a70140649a13
• omero_get_id was updated to 426415e73f46
• omero_get_value was updated to f5c4f523432d

QIIME 2

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

Annotation

• cpt_get_orfs was updated to f97bc7f587a1
• hhsearch was updated to 0dd6880ff950

ChemicalToolBox

• openbabel_remove_protonation_state was updated to 00263ca6ffb8

Mapping

• bioext_bealign was updated to 09dbbf5d3201
• bwameth was updated to b4e6819b25ef

Proteomics

• diann was updated to be5a0b2d8bd7
• openms_externalcalibration was updated to 61f5ad339398
• openms_openswathrewritetofeaturexml was updated to 5ad2d341fb2f
• openms_ticcalculator was updated to ed6c05e730de
• proteinortho_grab_proteins was updated to d348c3a151d9

FASTA/FASTQ

• fastx_clipper was updated to 90858c306551
• bbtools_bbduk was updated to 425dab0e057b
• bbtools_bbduk was updated to bf0cb5dd02f2
• fastp was updated to 3432a0e49b86

Mothur

• mothur_count_groups was updated to a0fc4eb349af
• mothur_count_seqs was updated to 014583f8e83b
• mothur_count_seqs was updated to 59a962f57cb5
• mothur_count_seqs was updated to 5a766fd3d23c
• mothur_count_seqs was updated to 7a6f9c899221
• mothur_count_seqs was updated to 9cfefba79f40
• mothur_count_seqs was updated to f00841c6fc14
• mothur_create_database was updated to 319884cd49a3
• mothur_create_database was updated to 34669a26ea47
• mothur_create_database was updated to 3cd1ccb4d58b
• mothur_create_database was updated to b6a0f2e80e5d
• mothur_create_database was updated to e7e2fd373e8b
• mothur_degap_seqs was updated to 104cea550c2f
• mothur_degap_seqs was updated to 1cbf0af70205
• mothur_degap_seqs was updated to 2393ecc7387c
• mothur_degap_seqs was updated to 36d252955070
• mothur_degap_seqs was updated to a7fced14ce99
• mothur_deunique_seqs was updated to 0369aff1be76
• mothur_deunique_seqs was updated to 276c9f17a9a2
• mothur_deunique_seqs was updated to 5faf0506611f
• mothur_deunique_seqs was updated to 73aeeac872d7
• mothur_deunique_seqs was updated to 77e034e33a66
• mothur_deunique_seqs was updated to f6c604b2793e
• mothur_deunique_tree was updated to 1ace9d6863aa
• mothur_deunique_tree was updated to 2b96ca0b44c0
• mothur_deunique_tree was updated to 50a228ab91a3
• mothur_deunique_tree was updated to 98083c5a4338
• mothur_deunique_tree was updated to d247213cebfc
• mothur_deunique_tree was updated to ec5e03c0f18e
• mothur_dist_seqs was updated to 0554c9338ca0
• mothur_dist_seqs was updated to 10f5ecfab7bb
• mothur_dist_seqs was updated to 31a3b2112418
• mothur_dist_seqs was updated to 502323efbd82
• mothur_dist_seqs was updated to dcbf475d7d60
• mothur_dist_shared was updated to 1a899fec55e1
• mothur_dist_shared was updated to 342a2b68ec4f
• mothur_dist_shared was updated to 3e2ca0c67e9d
• mothur_dist_shared was updated to 5d6d9f0d0652
• mothur_dist_shared was updated to 6290d3234345
• mothur_dist_shared was updated to f25598da7174
• mothur_fastq_info was updated to 1edab4936153
• mothur_fastq_info was updated to 25f02dced96c
• mothur_fastq_info was updated to 3ce3974a0e0b
• mothur_fastq_info was updated to a630c5167f5d
• mothur_fastq_info was updated to ab2c5805894a
• mothur_fastq_info was updated to f02f3ca6dfd1
• mothur_filter_seqs was updated to 89b9efa3c1f0
• mothur_filter_seqs was updated to a0ce9fb3f260
• mothur_filter_seqs was updated to b587a3a485b8
• mothur_filter_seqs was updated to daccf69bc281
• mothur_filter_seqs was updated to e71c69acde3f
• mothur_filter_shared was updated to 007311ce6297
• mothur_filter_shared was updated to 2d1dbf69f589
• mothur_filter_shared was updated to 382b60f3756e
• mothur_filter_shared was updated to 38bb70251d7a
• mothur_filter_shared was updated to 79f24f4ee6b6
• mothur_filter_shared was updated to e44c38a17c7a
• mothur_get_communitytype was updated to 4e708ec53432
• mothur_get_communitytype was updated to 79dc573692a4
• mothur_get_communitytype was updated to ad6d51c51be2
• mothur_get_communitytype was updated to beb4e0832f3b
• mothur_get_communitytype was updated to f84ff9e03568
• mothur_get_coremicrobiome was updated to 42244e3619cf
• mothur_get_coremicrobiome was updated to 618612060af3
• mothur_get_coremicrobiome was updated to 80b24979c575
• mothur_get_coremicrobiome was updated to 820a106991a5
• mothur_get_coremicrobiome was updated to ae1411cffbee
• mothur_get_dists was updated to 4d0f7df5a8f8
• mothur_get_dists was updated to 6936b18e2a9e
• mothur_get_dists was updated to be90a8fc5b76
• mothur_get_dists was updated to c8fbbada97dc
• mothur_get_dists was updated to d1fba6b01a90
• mothur_get_group was updated to 081d0fbf9751
• mothur_get_group was updated to 467378f04253
• mothur_get_group was updated to 65d9f4688890
• mothur_get_group was updated to 83700d313432
• mothur_get_group was updated to f220bbab51e1
• mothur_get_group was updated to f2b626fe7082
• mothur_get_groups was updated to 506e6a44cc68
• mothur_get_groups was updated to b1c35f71607f
• mothur_get_groups was updated to cfeef38a433e
• mothur_get_groups was updated to dd84e5f5eeaa
• mothur_get_groups was updated to e4d70a26c19f
• mothur_get_label was updated to 07d9a6a72e6d
• mothur_get_label was updated to 78e5065b27bd
• mothur_get_label was updated to 80b791e2a7bd
• mothur_get_label was updated to bb8b69e90604
• mothur_get_label was updated to c0a77971f496
• mothur_get_label was updated to ee13e5a4f9f3
• mothur_get_lineage was updated to 0bbfc05d924e
• mothur_get_lineage was updated to 563718e09fa8
• mothur_get_lineage was updated to 65853cd9ac99
• mothur_get_lineage was updated to d1abc038d4bd
• mothur_get_lineage was updated to dcecfbcf1edd
• mothur_get_mimarkspackage was updated to 49f2db40374d
• mothur_get_mimarkspackage was updated to 6dbc31423c24
• mothur_get_mimarkspackage was updated to 9983b77b0532
• mothur_get_mimarkspackage was updated to cd624927e763
• mothur_get_otulabels was updated to 6b173f5aa3ca
• mothur_get_otulabels was updated to 78168125a0c0
• mothur_get_otulabels was updated to b847275dfdf2
• mothur_get_otulabels was updated to fd62ac4a6b84
• mothur_get_otulist was updated to 2478fb777d97
• mothur_get_otulist was updated to 903acbb547c0
• mothur_get_otulist was updated to a68c119c37c5
• mothur_get_otulist was updated to ef6e35325002
• mothur_get_otulist was updated to f0cf508cdc98
• mothur_get_oturep was updated to 1e1a6eaae624
• mothur_get_oturep was updated to 5e43c9229eda
• mothur_get_oturep was updated to 648b3da84b07
• mothur_get_oturep was updated to 782220733828
• mothur_get_oturep was updated to f821624d355c
• mothur_get_otus was updated to 278a9f09614c
• mothur_get_otus was updated to 71d3e589c0b1
• mothur_get_otus was updated to 8a67e60260ca
• mothur_get_otus was updated to 971ab18e74d7
• mothur_get_otus was updated to 976e1434503d
• mothur_get_otus was updated to dbb1bc225df1
• mothur_get_rabund was updated to 08a740b388d8
• mothur_get_rabund was updated to 7792e8e95112
• mothur_get_rabund was updated to 8ddccb25fcc6
• mothur_get_rabund was updated to bd695645069f
• mothur_get_relabund was updated to 6b3130958acc
• mothur_get_relabund was updated to 7756edb68ddc
• mothur_get_relabund was updated to b07e7be6326a
• mothur_get_relabund was updated to d53c7d63b940
• mothur_get_relabund was updated to ed294552b627
• mothur_get_sabund was updated to 0bc1dc0c6aad
• mothur_get_sabund was updated to 132ec4ee9d17
• mothur_get_sabund was updated to 4ebedd866934
• mothur_get_sabund was updated to a41ba5f5f6b8
• mothur_get_seqs was updated to 32a95d4cd850
• mothur_get_seqs was updated to 8b8c7cf6738c
• mothur_get_seqs was updated to d3906a9c70c4
• mothur_get_seqs was updated to f31e3b8f2336
• mothur_get_seqs was updated to f5cb275acba9
• mothur_get_seqs was updated to fc4b74b7f345
• mothur_get_sharedseqs was updated to 32040fb8ffdf
• mothur_get_sharedseqs was updated to 414307889d75
• mothur_get_sharedseqs was updated to 67faa6dacbae
• mothur_get_sharedseqs was updated to deb8f26d8d66
• mothur_get_sharedseqs was updated to f8bf3dd4db47
• mothur_heatmap_bin was updated to 416182d7281c
• mothur_heatmap_bin was updated to 83d3c6dba0b1
• mothur_heatmap_bin was updated to 921a072b8552
• mothur_heatmap_bin was updated to a271eda55001
• mothur_heatmap_bin was updated to aeacbc9d5333
• mothur_heatmap_sim was updated to 0674bdcb3019
• mothur_heatmap_sim was updated to 24328bd746b5
• mothur_heatmap_sim was updated to 2f93c7bba6f8
• mothur_heatmap_sim was updated to 4e5640d04cab
• mothur_heatmap_sim was updated to c2dead9d38c4
• mothur_homova was updated to 68005ede9e6e
• mothur_homova was updated to 89054fe2207f
• mothur_homova was updated to 948d5731dbe0
• mothur_homova was updated to 9a215084d776
• mothur_homova was updated to ca2b0847c8a2
• mothur_homova was updated to d17fe3c8a489
• mothur_indicator was updated to 0232e2fe594c
• mothur_indicator was updated to 1c6dadf7bc72
• mothur_indicator was updated to 39750697d7a6
• mothur_indicator was updated to a224c578d941
• mothur_indicator was updated to b876b3c1690b
• mothur_indicator was updated to ba8150cff807
• mothur_lefse was updated to 008cb5a481f2
• mothur_lefse was updated to 7691a4b846fc
• mothur_lefse was updated to 772e6a5b7358
• mothur_lefse was updated to c98e47f7b233
• mothur_lefse was updated to ccd1ce71c11f
• mothur_lefse was updated to d47a909185ef
• mothur_libshuff was updated to 1cd0f3241d5b
• mothur_libshuff was updated to 1fe5098be27a
• mothur_libshuff was updated to 45a78bb8819d
• mothur_libshuff was updated to 7c46233bfa06
• mothur_libshuff was updated to cda3d2247a7b
• mothur_libshuff was updated to eefbe872fd04
• mothur_list_otulabels was updated to 0c9eb32683bf
• mothur_list_otulabels was updated to 1c8906cc1ddd
• mothur_list_otulabels was updated to 5e366a0379e6
• mothur_list_otulabels was updated to 72c4cd2b5b74
• mothur_list_otulabels was updated to c2d81e2bf502
• mothur_list_otulabels was updated to e643cc6c39cb
• mothur_list_seqs was updated to 0ad4a88e6314
• mothur_list_seqs was updated to 3612e382d294
• mothur_list_seqs was updated to 6c2a5ff159ff
• mothur_list_seqs was updated to 9b600578c108
• mothur_list_seqs was updated to ea1a32c7927e
• mothur_make_biom was updated to 143cd841de28
• mothur_make_biom was updated to 55e975c9a012
• mothur_make_biom was updated to b0605e49d01c
• mothur_make_biom was updated to cfdfa41e01a4
• mothur_make_biom was updated to e29c05b88096
• mothur_make_biom was updated to ecd90b4198a2
• mothur_make_contigs was updated to 00dd059b77e5
• mothur_make_contigs was updated to 4b72b6c43327
• mothur_make_contigs was updated to 4e9136c2c4c3
• mothur_make_contigs was updated to 829bb93d3add
• mothur_make_contigs was updated to c3203178c41f
• mothur_make_contigs was updated to f65c34178487
• mothur_make_design was updated to 185c17f84d91
• mothur_make_design was updated to 4228d1b7aa01
• mothur_make_design was updated to 4405d0fbfada
• mothur_make_design was updated to 4b18c3d54bc6
• mothur_make_design was updated to 6ec3ec95ae68
• mothur_make_fastq was updated to 1684157db3c1
• mothur_make_fastq was updated to 25b9449a5f3d
• mothur_make_fastq was updated to 97587d4961a0
• mothur_make_fastq was updated to e6a7eaf1923d
• mothur_make_fastq was updated to e9b12c5ad27f
• mothur_make_fastq was updated to f09c0a3bf8b9
• mothur_make_group was updated to 182b471ed56b
• mothur_make_group was updated to 63a75db03ecc
• mothur_make_group was updated to 7ea39cdd3c5d
• mothur_make_group was updated to afc13b55ead3
• mothur_make_group was updated to c7ac82d16b14
• mothur_make_lefse was updated to 2da52b4bf3dc
• mothur_make_lefse was updated to 678c90b43e17
• mothur_make_lefse was updated to 88be2167f369
• mothur_make_lefse was updated to b009f1b8e922
• mothur_make_lefse was updated to c714d0aa5afa
• mothur_make_lookup was updated to 23c1af22331b
• mothur_make_lookup was updated to 4dd1404ee026
• mothur_make_lookup was updated to a33258dc5bf8
• mothur_make_lookup was updated to b41d69df69ac
• mothur_make_lookup was updated to d20ab289b0c0
• mothur_make_lookup was updated to d56e5a7a9cef
• mothur_make_shared was updated to 0851ae17c58e
• mothur_make_shared was updated to 5eaf2d7253f6
• mothur_make_shared was updated to 60f0853e33f3
• mothur_make_shared was updated to b5f98810181e
• mothur_make_shared was updated to f7a10f16aa99
• mothur_make_shared was updated to fdebbe239529
• mothur_make_sra was updated to 2341a1066c67
• mothur_make_sra was updated to abb205c9b967
• mothur_make_sra was updated to afa357a7b58a
• mothur_make_sra was updated to bf608ff56ecf
• mothur_mantel was updated to 17b471efdc40
• mothur_mantel was updated to 1ef479343cfe
• mothur_mantel was updated to 3179a29d3b70
• mothur_mantel was updated to b0f1e033e18d
• mothur_mantel was updated to bcc475f1af4a
• mothur_mantel was updated to ea41c6924945
• mothur_merge_files was updated to 129646af86bc
• mothur_merge_files was updated to 12b1bd17d614
• mothur_merge_files was updated to 21a9274337f5
• mothur_merge_files was updated to 7bd37d6decd9
• mothur_merge_files was updated to 80e3857bf744
• mothur_merge_files was updated to f5dba396fe63
• mothur_merge_groups was updated to 052bc33e134e
• mothur_merge_groups was updated to 23d11599dfaf
• mothur_merge_groups was updated to 41bba0dfdbe0
• mothur_merge_groups was updated to 47d3c31340d7
• mothur_merge_groups was updated to ddd068a49efe
• mothur_merge_groups was updated to f170676a1d12
• mothur_merge_sfffiles was updated to 0778c4b6a300
• mothur_merge_sfffiles was updated to 26ddda2d2462
• mothur_merge_sfffiles was updated to 4484fe89e1a5
• mothur_merge_sfffiles was updated to b296d6f25ee3
• mothur_merge_sfffiles was updated to ec717c8dce9b
• mothur_merge_taxsummary was updated to 3a2ee62cb710
• mothur_merge_taxsummary was updated to 41f056a2ca71
• mothur_merge_taxsummary was updated to 43b27677d1d0
• mothur_merge_taxsummary was updated to a2dda99b6d79
• mothur_metastats was updated to 19836a38dc20
• mothur_metastats was updated to 6adb9311e99d
• mothur_metastats was updated to 7c209dbe20b8
• mothur_metastats was updated to f50fa0018f6f
• mothur_metastats was updated to fe9f4a0d61d3
• mothur_mimarks_attributes was updated to 247d1bacbefe
• mothur_mimarks_attributes was updated to 5106f3ce22a3
• mothur_mimarks_attributes was updated to 7986e1c4bc23
• mothur_mimarks_attributes was updated to 8354a02a83e1
• mothur_mimarks_attributes was updated to b9fe5cf8f2bc
• mothur_mimarks_attributes was updated to bfbd98549bc4
• mothur_nmds was updated to 3cc04a065490
• mothur_nmds was updated to 555a89f14c55
• mothur_nmds was updated to 98f1cc2bc428
• mothur_nmds was updated to a81680d1db78
• mothur_nmds was updated to f36dc56e8a2b
• mothur_nmds was updated to f65e0350ef5d
• mothur_normalize_shared was updated to 4bdf28c910af
• mothur_normalize_shared was updated to 5a00f7d92dc2
• mothur_normalize_shared was updated to a89fbfe8386f
• mothur_normalize_shared was updated to a8bc62f05cfa
• mothur_normalize_shared was updated to ad80d646ed1c
• mothur_otu_association was updated to 0037bed5bf77
• mothur_otu_association was updated to 12af8c375bb8
• mothur_otu_association was updated to a02117aa58a5
• mothur_otu_association was updated to a2511c40e7b8
• mothur_otu_association was updated to ffbe8c8baaf9
• mothur_otu_hierarchy was updated to 0161571cd8f8
• mothur_otu_hierarchy was updated to 693fbc55f70e
• mothur_otu_hierarchy was updated to 98abd0047263
• mothur_otu_hierarchy was updated to abf3d41b7428
• mothur_otu_hierarchy was updated to f9326e93f5c3
• mothur_pairwise_seqs was updated to 39c7213ca279
• mothur_pairwise_seqs was updated to 4a73df58d56b
• mothur_pairwise_seqs was updated to 6adf5871ec0b
• mothur_pairwise_seqs was updated to bc53948e3666
• mothur_pairwise_seqs was updated to c05906ab8c41
• mothur_pairwise_seqs was updated to cfe04aa12a39
• mothur_parse_list was updated to 408650f291f7
• mothur_parse_list was updated to 59906aed724a
• mothur_parse_list was updated to 94d78559a361
• mothur_parse_list was updated to 99579d05a632
• mothur_parse_list was updated to accd70ff66e6
• mothur_parsimony was updated to 65955ae23f29
• mothur_parsimony was updated to 70d555c67aec
• mothur_parsimony was updated to aff64115d95f
• mothur_parsimony was updated to da7f70ebfb4c
• mothur_parsimony was updated to dd1a7b862fab
• mothur_parsimony was updated to fd6cebeaa143
• mothur_pca was updated to 46689a444f2b
• mothur_pca was updated to 7474b222205d
• mothur_pca was updated to 74d1b765843b
• mothur_pca was updated to 9f3da360714c
• mothur_pca was updated to e3638c927d93
• mothur_pca was updated to ee26037477a1
• mothur_pcoa was updated to 1c1d69d94f7d
• mothur_pcoa was updated to 485e149a8aba
• mothur_pcoa was updated to 539f247ff952
• mothur_pcoa was updated to 5bc3e30e1d9e
• mothur_pcoa was updated to 64f54fb804b3
• mothur_pcoa was updated to c9fc98593dec
• mothur_pcr_seqs was updated to 0a23bfe005be
• mothur_pcr_seqs was updated to 0ce27975e549
• mothur_pcr_seqs was updated to 482d26a40589
• mothur_pcr_seqs was updated to 4dbfdaaa6a05
• mothur_pcr_seqs was updated to 7dba7376870c
• mothur_phylo_diversity was updated to 20b1d5bb66d0
• mothur_phylo_diversity was updated to c76d9ea84d39
• mothur_phylo_diversity was updated to c7d41770f4ce
• mothur_phylo_diversity was updated to e398beade8e7
• mothur_phylo_diversity was updated to ef55ccbfb725
• mothur_phylotype was updated to 12e24ffced04
• mothur_phylotype was updated to 249cdeb3cdb1
• mothur_phylotype was updated to 4d219b4dfd6a
• mothur_phylotype was updated to 551a2d9c0aa7
• mothur_phylotype was updated to 58f143161d30
• mothur_phylotype was updated to e301ed7e04d8
• mothur_pre_cluster was updated to 05183ee20cf8
• mothur_pre_cluster was updated to 872dbea91d49
• mothur_pre_cluster was updated to baba9fff9dba
• mothur_pre_cluster was updated to d848e23e9343
• mothur_pre_cluster was updated to ed67052d4285
• mothur_pre_cluster was updated to fbbe2b081299
• mothur_primer_design was updated to 0b63f5faf6e5
• mothur_primer_design was updated to 487977c2c586
• mothur_primer_design was updated to 6e8cdd7e6825
• mothur_primer_design was updated to aa4dcd3099fe
• mothur_primer_design was updated to d6f7c58a89d0
• mothur_primer_design was updated to eecf8144be3a
• mothur_rarefaction_shared was updated to 2175b62675ed
• mothur_rarefaction_shared was updated to 325ecaad64c0
• mothur_rarefaction_shared was updated to 419266a5e29e
• mothur_rarefaction_shared was updated to 50312cd2fc7a
• mothur_rarefaction_shared was updated to 76149f899b5c
• mothur_rarefaction_shared was updated to f58d1c616fb7
• mothur_rarefaction_single was updated to 57e3e6bf2e41
• mothur_rarefaction_single was updated to 5c2157147393
• mothur_rarefaction_single was updated to 8091da04fbac
• mothur_rarefaction_single was updated to af521db77c56
• mothur_rarefaction_single was updated to b5bcc4bf53d1
• mothur_rarefaction_single was updated to ebb853546cac
• mothur_remove_dists was updated to 11795a719c90
• mothur_remove_dists was updated to ad18e40e8569
• mothur_remove_dists was updated to b55a870c95aa
• mothur_remove_dists was updated to f7dba43ea52c
• mothur_remove_groups was updated to 2d5258c52be0
• mothur_remove_groups was updated to 3fac82ad3f01
• mothur_remove_groups was updated to 7c5b7dddd02e
• mothur_remove_groups was updated to b0748ba87fba
• mothur_remove_groups was updated to fae57cd6cc12
• mothur_remove_lineage was updated to 2a4d6c3d9b6d
• mothur_remove_lineage was updated to 2f633c057c0d
• mothur_remove_lineage was updated to 380e75c0ae8e
• mothur_remove_lineage was updated to 5a41ab037c7c
• mothur_remove_lineage was updated to c03e5575b636
• mothur_remove_otulabels was updated to 1f6046c0efdd
• mothur_remove_otulabels was updated to 2cbf56d15f4b
• mothur_remove_otulabels was updated to 5133ef623148
• mothur_remove_otulabels was updated to 9557cc0613de
• mothur_remove_otulabels was updated to b9e2724e9fc7
• mothur_remove_otus was updated to 0e73681a7cdc
• mothur_remove_otus was updated to 38c03ac3d622
• mothur_remove_otus was updated to 530698de365d
• mothur_remove_otus was updated to 6bdb704814f4
• mothur_remove_otus was updated to d0b2ec5b9a25
• mothur_remove_rare was updated to 196b1583580a
• mothur_remove_rare was updated to 2531a323f0c2
• mothur_remove_rare was updated to 33366e3a6099
• mothur_remove_rare was updated to 7b6e00f6c21f
• mothur_remove_rare was updated to 9ac808d4e0b5
• mothur_remove_rare was updated to da5fbab58754
• mothur_remove_seqs was updated to 2fa446f85b18
• mothur_remove_seqs was updated to 5097ac2cbfc3
• mothur_remove_seqs was updated to 92eb629218e1
• mothur_remove_seqs was updated to 9480bbc368c0
• mothur_remove_seqs was updated to 955ae21bc7e1
• mothur_remove_seqs was updated to eec15ff2d3c9
• mothur_reverse_seqs was updated to 03450507aa98
• mothur_reverse_seqs was updated to 0ca1d45851ee
• mothur_reverse_seqs was updated to be74be7f5d90
• mothur_reverse_seqs was updated to db762c766b89
• mothur_reverse_seqs was updated to f7f5cd1ae299
• mothur_screen_seqs was updated to 595419d427b6
• mothur_screen_seqs was updated to 94d8dbac60d8
• mothur_screen_seqs was updated to a136fc12b26a
• mothur_screen_seqs was updated to c1feef4d5e34
• mothur_sens_spec was updated to 084dc4e8caae
• mothur_sens_spec was updated to 27171cf0b8ba
• mothur_sens_spec was updated to 5ff10ccd7100
• mothur_sens_spec was updated to b36825c79054
• mothur_sens_spec was updated to c3f0b847dc40
• mothur_sens_spec was updated to ddda05cfccb4
• mothur_seq_error was updated to 2851c368b879
• mothur_seq_error was updated to a03c9ebf1959
• mothur_seq_error was updated to bb53c2c29c23
• mothur_seq_error was updated to c8a364414b34
• mothur_seq_error was updated to cd31c11bcc25
• mothur_sffinfo was updated to 09e3b0966a11
• mothur_sffinfo was updated to 3839397c8f28
• mothur_sffinfo was updated to 387d9e58afc2
• mothur_sffinfo was updated to 8b42e4ec39df
• mothur_sffinfo was updated to f3a65ee4bfda
• mothur_shhh_flows was updated to 408595fde5c6
• mothur_shhh_flows was updated to 4e6cdbeaf3b5
• mothur_shhh_flows was updated to b6a88afacb17
• mothur_shhh_flows was updated to dfaf60f40e94
• mothur_shhh_flows was updated to fcb3fa45b93e
• mothur_shhh_seqs was updated to 151a711dec84
• mothur_shhh_seqs was updated to 6ee54b761c3c
• mothur_shhh_seqs was updated to aa189387c19c
• mothur_shhh_seqs was updated to d7e469b059da
• mothur_shhh_seqs was updated to e7327eaaab37
• mothur_shhh_seqs was updated to e963609595cc
• mothur_sort_seqs was updated to 2f6a9498447e
• mothur_sort_seqs was updated to 334476d3e35d
• mothur_sort_seqs was updated to 56bf9112c46b
• mothur_sort_seqs was updated to cbe644faff63
• mothur_sort_seqs was updated to d4c2eccb4f69
• mothur_sort_seqs was updated to fc60d2e290a4
• mothur_split_abund was updated to 246519916e6a
• mothur_split_abund was updated to 3a364dd93195
• mothur_split_abund was updated to cd7b11709aa9
• mothur_split_abund was updated to d665c913e26b
• mothur_split_abund was updated to d850b4b9659d
• mothur_split_abund was updated to fa40dca23957
• mothur_split_groups was updated to 53cbf80d4a65
• mothur_split_groups was updated to 618bf5d295e7
• mothur_split_groups was updated to 627cf4d36194
• mothur_split_groups was updated to 6d3d0936f910
• mothur_split_groups was updated to 99c44fc3cd32
• mothur_sub_sample was updated to 0f4dfa0332e8
• mothur_sub_sample was updated to 2986f7b01e74
• mothur_sub_sample was updated to 6c9215917d76
• mothur_sub_sample was updated to 893d9058d563
• mothur_summary_qual was updated to 11be0e5f3ebb
• mothur_summary_qual was updated to 315cf5ff78f9
• mothur_summary_qual was updated to 656ffc277a38
• mothur_summary_qual was updated to 6bf32768e15b
• mothur_summary_qual was updated to 86a40294e149
• mothur_summary_qual was updated to d50fdfdc2a0c
• mothur_summary_seqs was updated to 1a8e53763086
• mothur_summary_seqs was updated to 4041dc69af62
• mothur_summary_seqs was updated to 411ddfefe041
• mothur_summary_seqs was updated to 4af62516059b
• mothur_summary_seqs was updated to 609770e516fa
• mothur_summary_seqs was updated to d7ea2d0b4917
• mothur_summary_shared was updated to 47370a4efc95
• mothur_summary_shared was updated to 545234c1d925
• mothur_summary_shared was updated to 713806caf2cb
• mothur_summary_shared was updated to 74c8ebee088c
• mothur_summary_shared was updated to 81df36f90a1b
• mothur_summary_shared was updated to 8c18ced5e8c3
• mothur_summary_single was updated to 2857a688a7e9
• mothur_summary_single was updated to 782564664543
• mothur_summary_single was updated to 88d39b1679df
• mothur_summary_single was updated to de4801f05e5e
• mothur_summary_tax was updated to 4db7f1329d0e
• mothur_summary_tax was updated to bbff3370d740
• mothur_summary_tax was updated to c07510858fb0
• mothur_summary_tax was updated to c85146fe9890
• mothur_tree_shared was updated to 43e2715e98c9
• mothur_tree_shared was updated to 73dd30cbca20
• mothur_tree_shared was updated to ae1468c3e1fa
• mothur_tree_shared was updated to af2b5be87d4f
• mothur_tree_shared was updated to bf740ca1752a
• mothur_trim_flows was updated to 1f336ed182b8
• mothur_trim_flows was updated to 440c8d6fe21a
• mothur_trim_flows was updated to 45f3904bfdd2
• mothur_trim_flows was updated to 4d56c7e82ba6
• mothur_trim_flows was updated to 51da4c69105d
• mothur_trim_seqs was updated to 29dfb8d90999
• mothur_trim_seqs was updated to 38eea52b9ef7
• mothur_trim_seqs was updated to c49a6454726c
• mothur_trim_seqs was updated to dc318dec8b86
• mothur_trim_seqs was updated to fc17c9a3c800
• mothur_unifrac_unweighted was updated to 3597ca9089a5
• mothur_unifrac_unweighted was updated to 42ae7755f3c1
• mothur_unifrac_unweighted was updated to 46ba42ec466b
• mothur_unifrac_unweighted was updated to 6a622b34394a
• mothur_unifrac_unweighted was updated to dd62ea340aa7
• mothur_unifrac_weighted was updated to 09f802a2c3fa
• mothur_unifrac_weighted was updated to 20bc6be9e1df
• mothur_unifrac_weighted was updated to 7cb9b120fd44
• mothur_unifrac_weighted was updated to bf4b64c7d3e8
• mothur_unique_seqs was updated to 71788e5ced45
• mothur_unique_seqs was updated to 7c3f9c0850ac
• mothur_unique_seqs was updated to 84722a5b79af
• mothur_unique_seqs was updated to 8fce7ef726c8
• mothur_unique_seqs was updated to c50d04c78ecb
• mothur_unique_seqs was updated to d466580cd706
• mothur_venn was updated to 139bdc1c3b48
• mothur_venn was updated to 200defe4c42b
• mothur_venn was updated to 8df8d8b67b13
• mothur_venn was updated to b6bf3c22b503
• mothur_venn was updated to e4f4c1c0d193

Motif Tools

• meme_chip was updated to 091a9d638d78
• meme_fimo was updated to 0c5239d1aa65
• meme_fimo was updated to 4eb02864e5df
• meme_meme was updated to 3f0dd362b755
• meme_meme was updated to 9dd5373f6a5a
• meme_psp_gen was updated to a0fa4efeeee3
• meme_psp_gen was updated to ff2f53a32d0e

Multiple Alignments

• clustalw was updated to 4daabc25df00
• clustalw was updated to d9c2b2fde6a3
• chromeister was updated to a6d1f83c46b4
• mummer_mummer was updated to 26f2cc1cc1e9

NCBI Blast

• diamond was updated to 1e3323a44643
• diamond was updated to 20d92dc4c6cb

Nanopore

• medaka_consensus was updated to 0413e62b757a
• medaka_consensus was updated to 22f6a0e7424f
• medaka_consensus was updated to 5901bb391198
• medaka_consensus was updated to 682d1e2c8be4
• medaka_consensus was updated to 84dcccebad3d
• medaka_consensus was updated to b2aae698b9d3
• medaka_consensus was updated to eb1f4ba66dc6
• medaka_consensus was updated to fbf007713188
• medaka_consensus_pipeline was updated to 1ca4ce7241fd
• medaka_consensus_pipeline was updated to 2c72b8c09a70
• medaka_consensus_pipeline was updated to 35666d44fe7a
• medaka_consensus_pipeline was updated to a1b70f038b4a
• medaka_consensus_pipeline was updated to b35de691c42c
• medaka_consensus_pipeline was updated to d915879a88bc
• medaka_variant was updated to 3cde72a6e37c
• medaka_variant_pipeline was updated to 148f32860445
• medaka_variant_pipeline was updated to 5c959a2dde5f
• medaka_variant_pipeline was updated to 711d4deb7bdf
• medaka_variant_pipeline was updated to 7623e5888be9
• medaka_variant_pipeline was updated to ea1833858055
• medaka_variant_pipeline was updated to efca385ce679
• nanocompore_db was updated to ca9e70c0fef8
• nanocompore_sampcomp was updated to 25abc2c72ff9
• nanocompore_sampcomp was updated to 557cf45ff2c8
• nanocompore_sampcomp was updated to c43f4b80f5a9
• nanoplot was updated to db1eeffba23e
• nanopolishcomp_eventaligncollapse was updated to ad011fc670d6
• nanopolishcomp_freqmethcalculate was updated to 80b6e23cb70d
• ngmlr was updated to 95e4757d8da7
• ont_fast5_api_compress_fast5 was updated to 7147b894702a
• ont_fast5_api_fast5_subset was updated to 3bdd8fa109b1
• ont_fast5_api_multi_to_single_fast5 was updated to 1a37f742e7d7
• ont_fast5_api_single_to_multi_fast5 was updated to ceec541f4955
• pycoqc was updated to 3a2f2e24c37e
• pycoqc was updated to dc1500f42073

Operate on Genomic Intervals

• basecoverage was updated to 2cedec3759e4
• cluster was updated to 05696474ee89
• complement was updated to 38c8bb402872
• concat was updated to 35a89f8cc96e
• subtract was updated to 0145969324c4

Peak Calling

• macs was updated to f6319b0b4391
• macs2 was updated to c33686854b19

Phylogenetics

• hyphy_absrel was updated to 113854308427
• hyphy_absrel was updated to 181f5b9f139f
• hyphy_absrel was updated to 212c958f6cee
• hyphy_absrel was updated to 260a5a236b66
• hyphy_absrel was updated to 5a2b7f3d05e8
• hyphy_absrel was updated to 5f2ca10db92a
• hyphy_annotate was updated to 0cd45491b297
• hyphy_annotate was updated to 68cd2d8e3840
• hyphy_annotate was updated to a88848771d2d
• hyphy_annotate was updated to ad5901c44e66
• hyphy_annotate was updated to e6009f23582c
• hyphy_annotate was updated to ec59f7a36a24
• hyphy_annotate was updated to f7810488bd92
• hyphy_bgm was updated to 0286ee7cc27d
• hyphy_bgm was updated to 194108d6da22
• hyphy_bgm was updated to 1df765cc6bcb
• hyphy_bgm was updated to 31e1a5940620
• hyphy_bgm was updated to 5b6b8b08f1a9
• hyphy_bgm was updated to a54340ea0866
• hyphy_bgm was updated to a8ea0db2c606
• hyphy_bgm was updated to d1c977aee228
• hyphy_busted was updated to 1e712a6b98ff
• hyphy_busted was updated to 70fab57f3c05
• hyphy_busted was updated to 72b10710c4b7
• hyphy_busted was updated to cfbb255acb43
• hyphy_busted was updated to cff70490dbec
• hyphy_busted was updated to d6389faa75ff
• hyphy_busted was updated to e931e69b5a80
• hyphy_cfel was updated to 0990351232c6
• hyphy_cfel was updated to 4d712e32039e
• hyphy_cfel was updated to 5b63871000c9
• hyphy_cfel was updated to 643be54bef90
• hyphy_cfel was updated to 7a86c37f66d1
• hyphy_cfel was updated to fb833dd994f2
• hyphy_conv was updated to 1fdaf5c6a59f
• hyphy_conv was updated to 38755f5207a5
• hyphy_conv was updated to 3ea647006f17
• hyphy_conv was updated to 6569d04885e5
• hyphy_conv was updated to c1d24ff838c8
• hyphy_conv was updated to e98d40478b3e
• hyphy_conv was updated to f6e7b5955712
• hyphy_fade was updated to 5e8d0e777033
• hyphy_fade was updated to 7ae1a772f08e
• hyphy_fade was updated to 96817f0fd28b
• hyphy_fade was updated to a1a03eb66960
• hyphy_fade was updated to b959fd359a6b
• hyphy_fade was updated to d71d20c0ac09
• hyphy_fade was updated to eb23ebaf69d2
• hyphy_fade was updated to fccaa7ba05fd
• hyphy_fel was updated to 09afc9104fc8
• hyphy_fel was updated to 1b62167f7ab2
• hyphy_fel was updated to 1dc833581081
• hyphy_fel was updated to 2b1c3e81add3
• hyphy_fel was updated to 8276bb2adea5
• hyphy_fel was updated to 8a6ef85b934d
• hyphy_fel was updated to 8c9d8b5af4e4
• hyphy_fel was updated to d968c5dddfeb
• hyphy_fubar was updated to 099fc3ec12d2
• hyphy_fubar was updated to 1278a55205e5
• hyphy_fubar was updated to 55a45d4c31dc
• hyphy_fubar was updated to 600647840e87
• hyphy_fubar was updated to 6cb6a5e71ccb
• hyphy_fubar was updated to 93a0cf4ea5fc
• hyphy_fubar was updated to b2096be81d82
• hyphy_fubar was updated to cd41e7a4d35f
• hyphy_gard was updated to 053b20029378
• hyphy_gard was updated to 1fb98a84e86d
• hyphy_gard was updated to 26834f8534f9
• hyphy_gard was updated to 45d39a499816
• hyphy_gard was updated to 83f146502c0f
• hyphy_gard was updated to 8c388fd08c09
• hyphy_gard was updated to b8a7f604708e
• hyphy_gard was updated to bff9a82d630d
• hyphy_meme was updated to 0052303cfa41
• hyphy_meme was updated to 33040ebb30c6
• hyphy_meme was updated to 45a2366d777e
• hyphy_meme was updated to 5d8389d684bf
• hyphy_meme was updated to a114682b2788
• hyphy_meme was updated to d0f087aae1a3
• hyphy_meme was updated to d653a76f16ee
• hyphy_meme was updated to e0763df98352
• hyphy_prime was updated to 6d29207a32c5
• hyphy_prime was updated to b044a346c00d
• hyphy_prime was updated to b3b775a4ae1f
• hyphy_prime was updated to d8092fd69175
• hyphy_prime was updated to dc774be95f6c
• hyphy_prime was updated to e2942cd87117
• hyphy_prime was updated to f207757f9ca2
• hyphy_relax was updated to 134d46bd47dd
• hyphy_relax was updated to 3415a580926d
• hyphy_relax was updated to 4e9485eb5e9d
• hyphy_relax was updated to a4c5dc437558
• hyphy_relax was updated to be29e2137d32
• hyphy_relax was updated to d62d58407443
• hyphy_relax was updated to ed0f10a1db94
• hyphy_slac was updated to 0c6724c345d9
• hyphy_slac was updated to 24742f335426
• hyphy_slac was updated to 365e33adf3a4
• hyphy_slac was updated to 5f54f026fbe3
• hyphy_slac was updated to 67d3fc9ae1c3
• hyphy_slac was updated to 82c77ba28d70
• hyphy_slac was updated to 8522e7cc4fb4
• hyphy_slac was updated to c010cbc8ff3a
• hyphy_sm19 was updated to 00b4cf477625
• hyphy_sm19 was updated to 23b041c0d7d2
• hyphy_sm19 was updated to 36e40d93e8a3
• hyphy_sm19 was updated to 40e9160dbbbb
• hyphy_sm19 was updated to 50c12e254867
• hyphy_sm19 was updated to 86e10267b4cc
• hyphy_sm19 was updated to 87dd1c1c84d1
• hyphy_sm19 was updated to a96a307afb40
• hyphy_strike_ambigs was updated to 193dcaef2169
• hyphy_strike_ambigs was updated to 4bf743518e41
• hyphy_strike_ambigs was updated to 4e3212e05a8f
• hyphy_strike_ambigs was updated to 50554f806e16
• hyphy_strike_ambigs was updated to 650bcc9d3f36
• hyphy_strike_ambigs was updated to 79dc560d8ea3
• hyphy_strike_ambigs was updated to 7b214c69e387
• hyphy_summary was updated to 11dd1a96ffe9
• hyphy_summary was updated to 11fc6218365d
• hyphy_summary was updated to 81b23515db14
• hyphy_summary was updated to bd90215b7d15
• nextalign was updated to 41102a84e387
• nextalign was updated to d1dd7d1b07f6
• nextclade was updated to 07ab9bd68a02
• nextclade was updated to 0c46b95d60c3
• nextclade was updated to 128ba8da994f
• pangolin was updated to 0ec813ad2910
• pangolin was updated to 3a656a4a43ed
• pangolin was updated to 77402759b866
• pangolin was updated to debfccc4d65b
• pangolin was updated to fe3e8506112c
• phyml was updated to 850e213bee26
• raxml was updated to 14eb2acf30e3
• squirrel_phylo was updated to 46a0e11a7607
• squirrel_phylo was updated to b64098b87ea0
• squirrel_qc was updated to d8d5380422c1
• squirrel_qc was updated to f63d24309f49
• usher was updated to 335665e15630
• usher was updated to 524cb8f7a69a
• usher was updated to 8f6c7638eab2
• usher_matutils was updated to 52fd1d491417
• usher_matutils was updated to 79e2ee4e6ebb

Picard

• picard was updated to 2a17c789e0a5
• picard was updated to 585027e65f3b
• picard was updated to 6f9c0884a3e7

Quality Control

• multiqc was updated to 161f4383df15

RAD-seq

• stacks_assembleperead was updated to 0c741f364d18
• stacks_assembleperead was updated to 6eaf0f9836c8
• stacks_assembleperead was updated to b08cd32d03ad
• stacks_cstacks was updated to be3df81c0353
• stacks_cstacks was updated to dab92afa0c98
• stacks_denovomap was updated to 2b1dd7ab69f7
• stacks_denovomap was updated to 9f9d39f582f3
• stacks_denovomap was updated to eb1e95f88e96
• stacks_genotypes was updated to 00f4a4e553ae
• stacks_genotypes was updated to 46f061f3cfeb
• stacks_genotypes was updated to 5af94af9ec8f
• stacks_procrad was updated to 57910d476be9
• stacks_procrad was updated to 8fe258d72ff3
• stacks_procrad was updated to be78e39d56b3
• stacks_pstacks was updated to 67cbd80b83f5
• stacks_pstacks was updated to 7ebc7d229deb
• stacks_pstacks was updated to ede5223bc7f1
• stacks_refmap was updated to 1ba1185929c1
• stacks_refmap was updated to 4ee074ca88fb
• stacks_refmap was updated to 7c42e6768c41
• stacks_rxstacks was updated to 2360d8cf42f7
• stacks_rxstacks was updated to 3e43e51b3c3b
• stacks_rxstacks was updated to 9d0ac63dcfcd
• stacks_sstacks was updated to 95e37a28704b
• stacks_sstacks was updated to e38d181d4e72
• stacks_ustacks was updated to a4ec4f620a77
• stacks_ustacks was updated to b6de94f2edc0
• stacks_ustacks was updated to e5c97f09fe06

RNA Analysis

• salmon was updated to 6b0ba6de1424
• salmon was updated to b265be7af3db
• salmonquantmerge was updated to 178ebdfe5a7e
• salmonquantmerge was updated to 43658f594542
• salmonquantmerge was updated to 85b3dc9b6830
• cuffdiff was updated to af3e173cad7f
• cuffdiff was updated to d3ae7d9c2202
• cuffnorm was updated to f5b2ee725d34
• cuffquant was updated to 6dc45faebc1d
• brew3r_r was updated to 3198f52bffaa
• cherri_eval was updated to 5dd6b8c4ee1e
• cherri_train was updated to 2f7daa5d2d82
• chira_collapse was updated to 00187b27f5e5
• chira_extract was updated to 0a3107204741
• chira_extract was updated to 6977e9b7143d
• chira_extract was updated to 8b2c1d1556ac
• chira_map was updated to 92dbdc4d2722
• chira_map was updated to e7a9859e0040
• chira_merge was updated to 5db894671434
• chira_merge was updated to b8cb089a8e59
• chira_merge was updated to bd57d16524fe
• chira_quantify was updated to 1bfa8c091530
• chira_quantify was updated to 7fb3fc24be0e
• chira_quantify was updated to 8e3da3c5b851
• deseq2 was updated to 6f91b8ce6e07
• deseq2 was updated to 71bacea10eee
• deseq2 was updated to 9a616afdbda5
• deseq2 was updated to a416957ee305
• deseq2 was updated to de44f8eff84a
• deseq2 was updated to e5c8afac22a7
• dexseq was updated to 9fd8b69e6e68
• edger was updated to fb9b9f0f2f06
• featurecounts was updated to ce44c6f2ba38
• feelnc was updated to 095162ba8e90
• feelnc was updated to 17a77824c8e4
• heinz was updated to 704c401e0afb
• heinz was updated to e41ec5af7472
• idr was updated to d3ebbf39b1c5
• isoformswitchanalyzer was updated to b3f292d9f35d
• kallisto_pseudo was updated to 2953303df011
• kallisto_quant was updated to 60f888039fb2
• migmap was updated to fbbe507e692b
• qualimap_counts was updated to e020be4f281b
• scpipe was updated to 3ffca09599ca
• scpipe was updated to 5c4bca9dd4a2
• seurat was updated to 321bdd834266
• seurat was updated to 4c139a9415d7
• seurat was updated to 8d8412d35247
• seurat_clustering was updated to 94f1b9c7286f
• seurat_data was updated to 50c5abeb08ba
• seurat_integrate was updated to 4341b8ff2a46
• seurat_plot was updated to 2622dd85416f
• seurat_preprocessing was updated to c3170652bd98
• seurat_reduce_dimension was updated to e49429e8d6dd
• slamdunk was updated to 24657d5edede
• stringtie was updated to 333a6e13b622
• trinity was updated to 26d5493b20b6
• trinity was updated to 3772d9a10f27
• trinity was updated to 5b60313a6ce7
• trinity was updated to d5e8807a407d
• trinity_abundance_estimates_to_matrix was updated to 2e21a7c28b38
• trinity_abundance_estimates_to_matrix was updated to 400691c87530
• trinity_abundance_estimates_to_matrix was updated to 442e3696c634
• trinity_abundance_estimates_to_matrix was updated to 59fff1388bc2
• trinity_abundance_estimates_to_matrix was updated to 81a4697677e7
• trinity_abundance_estimates_to_matrix was updated to a009c96c5c18
• trinity_abundance_estimates_to_matrix was updated to cdde9062b49c
• trinity_align_and_estimate_abundance was updated to 00719b8004c9
• trinity_align_and_estimate_abundance was updated to 6c20d62180af
• trinity_align_and_estimate_abundance was updated to 6d6b72d14170
• trinity_align_and_estimate_abundance was updated to 75f4e1859ed7
• trinity_align_and_estimate_abundance was updated to 893655fa55f9
• trinity_align_and_estimate_abundance was updated to b2bbe9a7f1b8
• trinity_contig_exn50_statistic was updated to 03ca5ddc37a9
• trinity_contig_exn50_statistic was updated to 34840e9c79b0
• trinity_contig_exn50_statistic was updated to 41db7569b4ba
• trinity_contig_exn50_statistic was updated to 62b05e565a45
• trinity_contig_exn50_statistic was updated to b1e9a0355166
• trinity_contig_exn50_statistic was updated to beafdd47f8cf
• trinity_filter_low_expr_transcripts was updated to 1007cdb58d91
• trinity_filter_low_expr_transcripts was updated to 17101429bf0d
• trinity_filter_low_expr_transcripts was updated to 42c5172815f7
• trinity_filter_low_expr_transcripts was updated to a5ec0e79a93a
• trinity_filter_low_expr_transcripts was updated to aa38fa8c5815
• trinity_filter_low_expr_transcripts was updated to b10270739c1b
• trinity_gene_to_trans_map was updated to ba460ccf0006
• trinity_run_de_analysis was updated to 3bff7c3cf63c
• trinity_run_de_analysis was updated to ab87da55fe61
• trinity_run_de_analysis was updated to bbbb39ad9a7e
• trinity_run_de_analysis was updated to c63338cf419f
• trinity_run_de_analysis was updated to f3924bd07cba
• trinity_run_de_analysis was updated to fd588e138aa6
• trinity_super_transcripts was updated to 18a069ea4b96
• trinity_super_transcripts was updated to 29472bde8854
• trinity_super_transcripts was updated to 3064aa8755a0
• trinity_super_transcripts was updated to 6f480aee5877
• trinity_super_transcripts was updated to 9c545f1c1a4e
• trinity_super_transcripts was updated to b34de8dc0f64

Assembly

• rnaquast was updated to f89e3c318453

SAM/BAM

• bamtools_filter was updated to 4fe8a75334c8
• bamtools_filter was updated to bd735cae4ce6
• samtool_filter2 was updated to a7add3e93cc5
• samtool_filter2 was updated to b7aa423007bf
• samtools_calmd was updated to 3d873744df7e
• samtools_calmd was updated to c147e3a10573
• samtools_calmd was updated to c89806670ab9
• samtools_calmd was updated to e65c2cd0964c
• samtools_flagstat was updated to 4e404acfafa6
• samtools_idxstats was updated to 04d5581db1f5
• samtools_mpileup was updated to 111f83918fe6
• samtools_mpileup was updated to fa7ad9b89f4a
• samtools_phase was updated to 6166013090c0
• samtools_reheader was updated to d7b4851d1971
• samtools_rmdup was updated to 9129584416e2
• samtools_slice_bam was updated to b5c88b7b153e
• samtools_stats was updated to 47035d167365
• samtools_stats was updated to 793ad847121d
• samtools_stats was updated to e28839a4b932
• samtools_stats was updated to fed4aa48ba09
• ngsutils_bam_filter was updated to 49bf71fbc574
• ngsutils_bam_filter was updated to aecfe10118ed
• qualimap_multi_bamqc was updated to 16beb83e370c
• samtools_markdup was updated to d0a568e1904b
• samtools_merge was updated to 8890e2d4c068
• samtools_view was updated to df20f1fd453f
• tag_pileup_frequency was updated to b7d7ae3963aa

Send Data

• ena_upload was updated to e1b3b37aa69f

Single-cell

• alevin was updated to 04b494623f8e
• alevin was updated to 908a8d400fa2
• alevin was updated to 917f8e439160
• alevin was updated to c9944a2600f1
• alevin was updated to e53f19161c59
• anndata_export was updated to 83609ef746e9
• anndata_export was updated to c5ac926c838f
• anndata_export was updated to cfaf5a405371
• anndata_export was updated to e0395cca2c57
• anndata_import was updated to 499059586799
• anndata_import was updated to ae1e5d9d8972
• anndata_import was updated to d330b3082107
• anndata_import was updated to e175d4067b00
• anndata_inspect was updated to 0bf7fddf90c7
• anndata_inspect was updated to 33c0081e16c6
• anndata_inspect was updated to 383dcb0500f9
• anndata_inspect was updated to 6a1a3dab235a
• anndata_manipulate was updated to 7e8c677a7b71
• anndata_manipulate was updated to 8db95f488f0f
• anndata_manipulate was updated to a56baceb1900
• anndata_manipulate was updated to b03c60f8528f
• anndata_manipulate was updated to d1e49c3c0aa2
• cosg was updated to cf880680fd0b
• modify_loom was updated to 05631436cdf1
• modify_loom was updated to 0f1aaff9b22d
• modify_loom was updated to a7b951572609
• raceid_clustering was updated to 0bff0ee0683a
• raceid_clustering was updated to 4ea021bd7513
• raceid_clustering was updated to 528a43b1cbcf
• raceid_clustering was updated to ee0bbc160cb1
• raceid_filtnormconf was updated to 5d5b14dbd092
• raceid_filtnormconf was updated to b83fbc90161e
• raceid_inspectclusters was updated to 106718959281
• raceid_inspectclusters was updated to 20f522154663
• raceid_inspectclusters was updated to 9fec5dd8fbb9
• raceid_inspectclusters was updated to f3eb2291da05
• raceid_inspecttrajectory was updated to 5156383d3a5d
• raceid_inspecttrajectory was updated to 86e2358cf273
• raceid_inspecttrajectory was updated to a6821f856a1e
• raceid_inspecttrajectory was updated to e0e9b24d76aa
• raceid_trajectory was updated to 2af7c5086a96
• raceid_trajectory was updated to 3e5bb16abb55
• raceid_trajectory was updated to 87de515af823
• raceid_trajectory was updated to ff7cd3c7c1df
• scanpy_cluster_reduce_dimension was updated to 178242b82297
• scanpy_cluster_reduce_dimension was updated to 35bc2eb568ed
• scanpy_cluster_reduce_dimension was updated to 3e4e1cf73d98
• scanpy_cluster_reduce_dimension was updated to 64ff3ef24fae
• scanpy_cluster_reduce_dimension was updated to 6f2d2c7f77ee
• scanpy_cluster_reduce_dimension was updated to 766be978777a
• scanpy_cluster_reduce_dimension was updated to 8983e7a04ba7
• scanpy_filter was updated to 5511647110ff
• scanpy_filter was updated to 5b3c1679d29b
• scanpy_filter was updated to 713a0c65b1fe
• scanpy_filter was updated to 8b9610ab366a
• scanpy_filter was updated to a72e9faea895
• scanpy_filter was updated to aa0059118fb9
• scanpy_filter was updated to f87ed6503715
• scanpy_inspect was updated to 08192eebb47d
• scanpy_inspect was updated to 4338bf96809e
• scanpy_inspect was updated to 9d1997b08ed6
• scanpy_inspect was updated to 9d33775ec67d
• scanpy_inspect was updated to ca086f24422f
• scanpy_inspect was updated to d1cd8c147809
• scanpy_inspect was updated to e4c99c83dfbf
• scanpy_normalize was updated to 4bda4412b8c2
• scanpy_normalize was updated to 51d945eab1e1
• scanpy_normalize was updated to 5342ce58cd1e
• scanpy_normalize was updated to 55f2212bb675
• scanpy_normalize was updated to 5dada6f76047
• scanpy_normalize was updated to ec32793ce1dd
• scanpy_normalize was updated to f3ad813a58a3
• scanpy_plot was updated to 2dfb2227a16c
• scanpy_plot was updated to 62acdd96d4a0
• scanpy_plot was updated to 70fa84e99463
• scanpy_plot was updated to 8599fd07d140
• scanpy_plot was updated to 9a169729c9f9
• scanpy_plot was updated to cb18f2388815
• scanpy_remove_confounders was updated to 524aa62a6066
• scanpy_remove_confounders was updated to 7a6701edcc92
• scanpy_remove_confounders was updated to 80d4e2cac903
• scanpy_remove_confounders was updated to 974bb00b2f43
• scanpy_remove_confounders was updated to b70219da4a96
• scanpy_remove_confounders was updated to c2ef03559dc6
• scanpy_remove_confounders was updated to c5541bfb8feb
• scanpy_remove_confounders was updated to e66884b1c1a5
• sceasy_convert was updated to 2062be7efc84
• sinto_barcode was updated to d0f56ac6bb60
• sinto_fragments was updated to 03a04f48b922
• snapatac2_clustering was updated to afb90d3485df
• snapatac2_peaks_and_motif was updated to 88192fe25375
• snapatac2_plotting was updated to 370d45e0d1a8
• snapatac2_preprocessing was updated to fef8f61cb34c

Statistics

• iwtomics_loadandplot was updated to 0027f3287b34
• iwtomics_loadandplot was updated to 8eb7dded0d52
• iwtomics_loadandplot was updated to ee7dd07a530e
• iwtomics_plotwithscale was updated to 25030f0d1154
• iwtomics_plotwithscale was updated to 4bd560127b68
• iwtomics_testandplot was updated to 800c7e974e3b
• iwtomics_testandplot was updated to 926cdd3158ae

Text Manipulation

• column_maker was updated to 427903d47026
• coverage was updated to 4ef9819dc7fb
• flanking_features was updated to a09d13b108fd
• intersect was updated to 33b3f3688db4
• join was updated to a10f49d9218a
• merge was updated to 381cd27bf67a
• tables_arithmetic_operations was updated to 82fa5062d611
• filter_tabular was updated to 4d5aae46f850
• gff3_rebase was updated to 238981ed43b7
• gff3_rebase was updated to e54940ea270c
• gff3_rebase was updated to ea35a85b941d
• table_compute was updated to 02c3e335a695
• table_compute was updated to 93a3ce78ce55
• table_compute was updated to cd36d6e45e29

Variant Calling

• freebayes was updated to 85dc96ebc770
• freebayes was updated to a7c9782130e8
• vcfcheck was updated to 2968c6916579
• vcffilter was updated to 9442e22779ca
• vcffilter was updated to de885f4afb7f
• vcffilter was updated to fa24bf0598f4
• vcfsort was updated to dd44c3f416c3
• vcfsort was updated to f0580efedada
• artic_guppyplex was updated to 76d6358f71b7
• artic_minion was updated to 7a7d7f30ddfc
• artic_minion was updated to f212134e204c
• artic_minion was updated to f5643712dca7
• bbtools_callvariants was updated to 8eace8923202
• bbtools_callvariants was updated to df9743790176
• bcftools_annotate was updated to 2436e3bef247
• bcftools_annotate was updated to 2958e3b49ad4
• bcftools_annotate was updated to 3f62d4939d54
• bcftools_annotate was updated to 403553ae19f6
• bcftools_annotate was updated to 95815a0bb307
• bcftools_call was updated to 072f606e2e69
• bcftools_call was updated to 3296c3680d96
• bcftools_call was updated to 4fa18320d29b
• bcftools_call was updated to 5801eff9ac7e
• bcftools_call was updated to 912a8ff07fc9
• bcftools_call was updated to cb30a39055d0
• bcftools_call was updated to d267bcfdc8fe
• bcftools_call was updated to f0d44631365f
• bcftools_cnv was updated to 13fe14c56f6d
• bcftools_cnv was updated to 143796b504eb
• bcftools_cnv was updated to 4891338c6c54
• bcftools_cnv was updated to 6d35a3780bfd
• bcftools_cnv was updated to 86737d0f7fab
• bcftools_cnv was updated to 8d637025a905
• bcftools_cnv was updated to b2d1b7dda2b7
• bcftools_concat was updated to 08296952d12f
• bcftools_concat was updated to 5ee777f9db23
• bcftools_concat was updated to 874cc12ae316
• bcftools_concat was updated to abd489215f73
• bcftools_concat was updated to d40d4bf05718
• bcftools_concat was updated to fc47ffec447e
• bcftools_consensus was updated to 1171446da5db
• bcftools_consensus was updated to 147de996e34f
• bcftools_consensus was updated to 70b8e9908ea8
• bcftools_consensus was updated to 92182c270ce4
• bcftools_consensus was updated to c82130967bd2
• bcftools_consensus was updated to d6dc477167f8
• bcftools_consensus was updated to edc3d484b99a
• bcftools_convert_from_vcf was updated to 34585fd4bd3e
• bcftools_convert_from_vcf was updated to 7cea7c7bf203
• bcftools_convert_from_vcf was updated to b8e9da766b0f
• bcftools_convert_from_vcf was updated to cacc9970727a
• bcftools_convert_from_vcf was updated to d58d2e8c7a57
• bcftools_convert_to_vcf was updated to 41873b29860a
• bcftools_convert_to_vcf was updated to 4935320a59a8
• bcftools_convert_to_vcf was updated to 7291189e98b4
• bcftools_convert_to_vcf was updated to c14b33ab15d8
• bcftools_convert_to_vcf was updated to fec517907949
• bcftools_csq was updated to 33df4e68959b
• bcftools_csq was updated to 40388f544e5d
• bcftools_csq was updated to 68216882a410
• bcftools_csq was updated to 8899a6d50699
• bcftools_csq was updated to e6f4badbe6f3
• bcftools_csq was updated to f01b2c9506b9
• bcftools_csq was updated to f10f5b4e7854
• bcftools_csq was updated to fdd127bd4a32
• bcftools_filter was updated to 5d6653c989cb
• bcftools_filter was updated to 656a916779fe
• bcftools_filter was updated to 6ca7c55a27e8
• bcftools_filter was updated to abafcb875ba6
• bcftools_filter was updated to e4988fd4d503
• bcftools_gtcheck was updated to 39810174657a
• bcftools_gtcheck was updated to 3eac729e66c9
• bcftools_gtcheck was updated to 64778f8899cc
• bcftools_gtcheck was updated to 672b6c02fbc7
• bcftools_gtcheck was updated to 91c1e57d5c7f
• bcftools_isec was updated to 02f349bdbf96
• bcftools_isec was updated to 15da1ddcfeff
• bcftools_isec was updated to 4afd849c9d35
• bcftools_isec was updated to 63aabc920911
• bcftools_isec was updated to 9ece72700ca9
• bcftools_merge was updated to 3e0e55c628b8
• bcftools_merge was updated to 798c063f8fc9
• bcftools_merge was updated to 9473302f4588
• bcftools_merge was updated to af163c712539
• bcftools_merge was updated to b84fda8ebef0
• bcftools_merge was updated to e03f2f3ac3a9
• bcftools_mpileup was updated to 03191140c66a
• bcftools_mpileup was updated to 0dbff46d5a1b
• bcftools_mpileup was updated to f59a4ab0e5b1
• bcftools_norm was updated to 1ca7418e46ee
• bcftools_norm was updated to 481476814acc
• bcftools_norm was updated to 76655fe2c70e
• bcftools_norm was updated to 93bdd3bf5743
• bcftools_norm was updated to a62e934346f5
• bcftools_norm was updated to c077f71d351f
• bcftools_norm was updated to ebb2e12a6de1
• bcftools_norm was updated to ff9e769ccd6c
• bcftools_plugin_color_chrs was updated to 05928e15da21
• bcftools_plugin_color_chrs was updated to 36960e552ddc
• bcftools_plugin_color_chrs was updated to 47ee1925fe9e
• bcftools_plugin_color_chrs was updated to 4e85a3a5dbd1
• bcftools_plugin_color_chrs was updated to 71dfde92fd57
• bcftools_plugin_color_chrs was updated to c39113e2ae34
• bcftools_plugin_color_chrs was updated to ebcd8649c621
• bcftools_plugin_color_chrs was updated to ee85030e893d
• bcftools_plugin_frameshifts was updated to 2e303fcd3b0c
• bcftools_plugin_frameshifts was updated to 399b40b2bcab
• bcftools_plugin_frameshifts was updated to 48ac4d611e92
• bcftools_plugin_frameshifts was updated to 58341ad4fb42
• bcftools_plugin_frameshifts was updated to 693d81b3e113
• bcftools_plugin_frameshifts was updated to a1c4d50c97e0
• bcftools_plugin_frameshifts was updated to c0b17fc737d4
• bcftools_plugin_frameshifts was updated to eb22990a2be9
• bcftools_plugin_setgt was updated to 262bba5b90ef
• bcftools_plugin_setgt was updated to 681bdf1e22ff
• bcftools_plugin_split_vep was updated to b317ccd39088
• bcftools_plugin_split_vep was updated to d55feecb6dc1
• bcftools_query was updated to 3b1b51e1fcba
• bcftools_query was updated to 94c5f302f0ea
• bcftools_query was updated to a850902cac64
• bcftools_query was updated to c9c5718edc19
• bcftools_query was updated to fdec14f69010
• bcftools_reheader was updated to 3b7b1fe7b937
• bcftools_reheader was updated to 6993b945aefc
• bcftools_reheader was updated to 8057cf55fa41
• bcftools_reheader was updated to 9ef52d95114b
• bcftools_reheader was updated to b3b3c060962e
• bcftools_roh was updated to 1a989b4110da
• bcftools_roh was updated to b76adb2f1c51
• bcftools_roh was updated to bdc67eeb0bc9
• bcftools_roh was updated to d80872078a09
• bcftools_roh was updated to fb3af223ff33
• bcftools_stats was updated to 80844da35ed5
• bcftools_stats was updated to a2f8dc22d7c0
• bcftools_stats was updated to bf8325a07ce7
• bcftools_stats was updated to c636e58df612
• bcftools_view was updated to 1d1762860d7e
• bcftools_view was updated to 98d5499ead46
• bcftools_view was updated to abc3ced31cd1
• bcftools_view was updated to c2ab91a0d506
• bcftools_view was updated to e15e4acae7ef
• bcftools_view was updated to e1a2389af238
• beacon2_biosamples was updated to 5fedf42a718b
• beacon2_biosamples was updated to 7cea4f9c4d8f
• beacon2_cohorts was updated to 8fc2c603a61f
• beacon2_cohorts was updated to d524bd42b89e
• beacon2_csv2xlsx was updated to ba4ed464f8b6
• beacon2_datasets was updated to 1f9f549aa9ca
• beacon2_datasets was updated to a38d4a52dbff
• beacon2_individuals was updated to 72d8cb0fa73f
• beacon2_individuals was updated to b648eb72552c
• beacon2_pxf2bff was updated to 30605b5fc43f
• beacon2_runs was updated to 016fc58daa80
• beacon2_runs was updated to 34814a1b0a3f
• beacon2_vcf2bff was updated to 0a757835a745
• beagle was updated to 563fd95fa88a
• cnvkit_access was updated to 25bba7640b06
• cnvkit_antitarget was updated to dd54b5c36317
• cnvkit_autobin was updated to 505e6bbaee59
• cnvkit_batch was updated to 97d2b6742760
• cnvkit_breaks was updated to 384fa596e5d9
• cnvkit_call was updated to 978ddcbedd60
• cnvkit_coverage was updated to 5699301a3bd1
• cnvkit_diagram was updated to 27ecb3477d34
• cnvkit_fix was updated to 49ecf6b6f9f4
• cnvkit_genemetrics was updated to 3e1d74c9e715
• cnvkit_heatmap was updated to 26554a14f841
• cnvkit_reference was updated to b45fa373a972
• cnvkit_scatter was updated to 02446206f574
• cnvkit_segment was updated to 33be231ce128
• cnvkit_segmetrics was updated to 86392285203a
• cnvkit_sex was updated to 0b34f56003dc
• cnvkit_target was updated to 428b93a3acb4
• delly_lr was updated to 7bd397ff21a2
• lofreq_alnqual was updated to 2953c43180c0
• lofreq_alnqual was updated to 606542a18f82
• lofreq_alnqual was updated to e0e2fd665102
• lofreq_call was updated to 31216d510164
• lofreq_filter was updated to 950d1d49d678
• lofreq_filter was updated to fdba1586551d
• lofreq_indelqual was updated to 2ae554b4bcca
• lofreq_indelqual was updated to 354b534eeab7
• lofreq_indelqual was updated to 5d6a078d30b0
• lofreq_viterbi was updated to af7e416d8176
• lofreq_viterbi was updated to ecd80c7c3886
• odgi_viz was updated to 536768de4748
• sansa_annotate was updated to 30079fa4e2fd
• sansa_annotate was updated to e3862632706d
• snippy was updated to 4df82423ba61
• snippy was updated to d220115f882b
• snippy was updated to feb7e635c6af
• snpeff was updated to 36dc3690a82c
• snpeff was updated to 479c4f2f4826
• snpeff was updated to 74aebe30fb52
• snpeff was updated to 9473cd297a76
• snpeff was updated to ca2b512e8d7c
• snpsift was updated to 2e497a770bca
• strelka_germline was updated to 1fbe84e8a740
• ucsc_fatovcf was updated to d9965e143053
• varscan_copynumber was updated to 0bc56f894766
• varscan_copynumber was updated to 192bd5b78300
• varscan_copynumber was updated to c24910ad5441
• varscan_copynumber was updated to e814a042315f
• varscan_mpileup was updated to 1e667badbe87
• varscan_mpileup was updated to 45288fb1f3f5
• varscan_mpileup was updated to 7c5e867820cf
• varscan_mpileup was updated to d7e6c347538d
• varscan_mpileup was updated to e3f170cc4f95
• varscan_somatic was updated to 31a38ce7e8ae
• varscan_somatic was updated to a57606054bd7
• vg_convert was updated to e68d9dfa62a2
• vg_view was updated to 95ec8f978762

Virology

• cooc_mutbamscan was updated to 9f1660129403
• cooc_tabmut was updated to 579538ff939d
• ivar_consensus was updated to 17f911830a8c
• ivar_consensus was updated to 2d9926ce62be
• ivar_consensus was updated to 3a72fede57ce
• ivar_consensus was updated to 5e668dc9f379
• ivar_consensus was updated to 731182d54f78
• ivar_consensus was updated to 7f781286b55f
• ivar_consensus was updated to d1459d85ff18
• ivar_consensus was updated to ede363a64152
• ivar_filtervariants was updated to 096a5b0210cc
• ivar_filtervariants was updated to 1ef5b6e3e09d
• ivar_filtervariants was updated to 2c47c138176e
• ivar_filtervariants was updated to 47a27906d750
• ivar_filtervariants was updated to 4abcfbc2e5b6
• ivar_filtervariants was updated to 51afc8a64951
• ivar_filtervariants was updated to b93845a04cc8
• ivar_filtervariants was updated to fcbeda41d0ac
• ivar_removereads was updated to 5dc33613c288
• ivar_removereads was updated to 69797fa273c3
• ivar_removereads was updated to 75c279fa403a
• ivar_removereads was updated to f57ce5d5c997
• ivar_trim was updated to 0893a1dbb807
• ivar_trim was updated to 28e4bcbc86e7
• ivar_trim was updated to a250929be21b
• ivar_trim was updated to cf65217ad61c
• ivar_variants was updated to 045d6d00f606
• ivar_variants was updated to 252dfb042563
• ivar_variants was updated to 3888bbe7a9ca
• ivar_variants was updated to aa9de8f20668
• ivar_variants was updated to abbc8041e8ec
• ivar_variants was updated to aea7008fe1f1
• read_it_and_keep was updated to 1563b58905f4

None

• data_manager_build_kraken2_database was updated to 9002633b4737
• data_manager_diamond_database_builder was updated to 4a08b7b76b78
• data_manager_gtdbtk_database_installer was updated to 2814c058a087
• data_manager_nextclade was updated to 4de9e77bcc9e

deepTools

• deeptools_alignmentsieve was updated to e5a296ce8fbb
• deeptools_bam_compare was updated to c89b665b45e4
• deeptools_bam_coverage was updated to 4df95152a39e
• deeptools_bam_pe_fragmentsize was updated to 3f9dc453c0e8
• deeptools_bigwig_compare was updated to 7989c6ddf634
• deeptools_compute_matrix was updated to 19bb3e6d9e31
• deeptools_compute_matrix_operations was updated to be95d48dd27f
• deeptools_correct_gc_bias was updated to 00a71ff7c06b
• deeptools_multi_bam_summary was updated to b4e53394fced
• deeptools_plot_correlation was updated to e44978659400
• deeptools_plot_enrichment was updated to 88ce7fed1488
• deeptools_plot_fingerprint was updated to ca8a7f0ea872
• deeptools_plot_heatmap was updated to 42cb23d80271
• deeptools_plot_pca was updated to 7784523d9743
• deeptools_plot_profile was updated to e9429e484e25

fetch_sequences___alignments

• extract_genomic_dna was updated to c8467246b57e
• extract_genomic_dna was updated to e400dcbc60d0