2022-9-24 UNITE was updated to 8.3 version (2021-5-10). Both fungi and eukaryote were added for RDP Classifier.

2021-12-24 Striped Unifrac is ready now. The SILVA database of 18S and 28S for RDP Classifier was updated to 138.1 version. Merry Christmas!

2021-12-3 PyNAST Alignment is ready now.

2021-12-3 Deblur is fixed and ready now.

2021-12-2 The following tools are temporarily removed due to incompatibility: Deblur, PyNast, Stripped Unifrac and FEAST.

2021-12-2 Galaxy upgrade is complete. Tax4Fun is now updated to Tax4Fun2. FUNGuild is now updated to version 1.2. FAPROTAX is now updated to version 1.2.4.

2021-11-19 One-Step PICRUSt2 pipeline is added in Section PICRUSt2. This tool is a standard pipeline for PICRUSt2. It requires FASTA and biom inputs and then runs all the steps automatically. If no advanced settings are required, this pipeline can be of use!"

2021-11-12 PR2 database (RDP Classifier) is updated to 4.14.0 version. See details: PR2 database release Github page.

2021-11-03 We added the parameter to '-maxaccepts 8 -maxrejects 256' for UPARSE and Unoise analysis, which will increase the sensitivity by reducing the number of false negatives but take more time to compute, please see details in termination options for USEARCH.

2021-10-15 A bug in 1) Sequence Placement (PICRUSt2) is fixed. The bug was reported to have led to error report (results shown in red) if there are sequences that cannot be appropriate placed in the tree. Now, the warning messages will be output to a result file called error log (empty file means no error). Besides, users can manually set the proportion of the total length of an input query sequence that must align with reference sequences.

2021-10-15 A bug in Translation (Translation and Clustering) is fixed. The bug was reported to have led to wrong results if reverse complementary sequence is used. We thank Wenli Shen for reporting this bug.

2021-5-15 PICRUSt2 is now available online. During test phase, PICRUSt will not be removed. If you find any bug in PICRUSt2 on Galaxy, please contact us for trouble shooting.

2021-5-4 It is reported that downloading large files might fail at times. For this, "File Compression (in Miscellaneous)" has been available to compress large file into smaller, easy-to-download size.

2021-4-30 RDP classifier is updated to 2.13 version. The databases for taxonomy classification are updated, including RDP training dataset (No. 18), SILVA (v138.1), and PR2 (v4.13).

2021-4-29 Some bias and mistakes in explanatory text in 'FEAST' have been fixed. Please make sure the format of input file is right as described.

2021-4-9 'Translation and Clustering' Toolbox is available now! The 4-step toolbox translates the nucleotide sequences into protein sequences and clusters them using Easy-Linclust from MMSeqs2. The cluster results can be summarized into OTU table form with the most abundance nucleotide sequence in each cluster selected to be the representative sequence. This toolbox is potentially useful for functional gene analysis.

2020-12-29 'Niche width analysis' is available now! This method calculates taxa niche width considering the environmental variables. Details can be found in Feng et al. Molecular Ecology. 2020.

2020-9-30 Three useful tools are added in Miscellaneous section: 'Count OTU Number Per sample' to quickly scan of total OTU reads for each sample, 'Transform a table' for quickly transforming tables, and 'Single Line Fasta Generator' to convert multiple sequence lines into single line in a FASTA file.

2019-11-7 A new section named "Functional genes sequences analysis tools" is online now! This section mainly includes basic preprocesses for sequences from raw sequencing data to OTU table generation.

2019-11-6 A new sub-section for 'Primer design and evaluation' can be found in the pipeline. It includes TrimAlignment, DegePrime, Coverage Calculation, Amplification Product Length and mFold for barcode and primer.

2019-11-5 CCA or RDA based Variation Partition Analysis (VPA) is added now. 2, 3, or 4 groups of environmental factors are all supported.

2019-7-26 "Fast expectation-maximization for microbialsource tracking (FEAST)" is online now! FEAST can be found in Source Tracker.

2019-7-25 "Calculate distance indexes 2" and "Calculate dissimilarity 2" are online now! Users can calculate different types of distance matrices (quantitative or presence/absence data) calculate dissimilarity with the matrices generated in "Calculate distance indexes 2". The programs are still improving and the old calculate distance indexes and dissimilarity test tools are still available.

2019-4-23 "MAFFT" is added for multiple sequences alignment.

2019-4-4 'Hierarchical Partitioning' is added in Statistics analysis tools - environment associations now!

2019-3-25 DADA2 analysis program is available now for OTU table generation.

2019-2-18 MiDAS (Microbial Database for Activated Sludge) was uploaded to 'shared library/16S data library' directory. This database mainly used for taxonomy assignment in this pipeline. Please use 'select own provided taxonomy database' and add FASTA file and TEXT file when running RDP Classifier.

2019-1-9 'Bipartite network for Samples and OTUs' was added in the Statistical analysis tools section. This program could generate bipartite network files between samples and their microbes according to OTU table.

2018-12-08 Striped Unifrac is implemented and can address large datasets. PCoA is available for own distance matrix. Phylogenetic alpha diversity can be calculated separately, including PD, MNTD, and MPD.

2018-12-06 The Protist Ribosomal Reference database (PR2, version 4.11.0) was added in the taxonomy classification (RDP classifier).

2018-12-04 FAPROTAX was updated to the newly version (v.1.1).

2018-11-01 The analysis procedure was updated.

2018-10-24 Large files (>4Gb) can be uploaded now.