# Latest **URL:** https://nextstrain.discourse.group/latest.md [Latest](https://nextstrain.discourse.group/latest.md) · [Categories](https://nextstrain.discourse.group/categories.md) --- ## [Welcome to nextstrain.discourse.group!](https://nextstrain.discourse.group/t/welcome-to-discussion-nextstrain-org/30)
**Author:** [@trs](https://nextstrain.discourse.group/u/trs)\ **Replies:** 17\ **Last updated:** [November 14, 2025, 3:14am UTC](https://nextstrain.discourse.group/t/welcome-to-discussion-nextstrain-org/30 "2025-11-14T03:14:13Z")
This website is intended to be a community forum for people using Nextstrain. We’re very interested to help public health and academic groups run Nextstrain analyses and share them (publicly or privately). The goal is to… --- ## [Advice on organizing wildcards phylogenetic workflow](https://nextstrain.discourse.group/t/advice-on-organizing-wildcards-phylogenetic-workflow/2270)
**Author:** [@eam](https://nextstrain.discourse.group/u/eam)\ **Replies:** 3\ **Last updated:** [September 23, 2026, 10:46pm UTC](https://nextstrain.discourse.group/t/advice-on-organizing-wildcards-phylogenetic-workflow/2270 "2026-09-23T22:46:17Z")
I am hoping to eventually create and maintain a Nextclade dataset of a currently unsupported pathogen and I’m looking for a little advice on how to organize the phylogenetic workflow. My pathogen has multiple subtypes an… --- ## [ToBRFV reference dataset in Nextclade](https://nextstrain.discourse.group/t/tobrfv-reference-dataset-in-nextclade/2268)
**Author:** [@Matelet](https://nextstrain.discourse.group/u/Matelet)\ **Replies:** 1\ **Last updated:** [September 8, 2026, 7:29pm UTC](https://nextstrain.discourse.group/t/tobrfv-reference-dataset-in-nextclade/2268 "2026-09-08T19:29:55Z")
Hello, First of all, thank you very much for developing and maintaining Nextstrain and Nextclade. These tools are extremely useful for our research, and we really appreciate the work that goes into making them available… --- ## [BDBV outbreak resources](https://nextstrain.discourse.group/t/bdbv-outbreak-resources/2267)
**Author:** [@nextstrain-team-bot](https://nextstrain.discourse.group/u/nextstrain-team-bot)\ **Replies:** 0\ **Last updated:** [September 2, 2026, 7:56pm UTC](https://nextstrain.discourse.group/t/bdbv-outbreak-resources/2267 "2026-09-02T19:56:29Z")
Since early May, researchers at the National Institute of Biomedical Research (INRB) and their partners have been sequencing isolates from the ongoing Bundibugyo ebolavirus outbreak in the DRC. Together with the INRB, w… --- ## [Looking for the best way to organize presentation files with Nextstrain tutorials](https://nextstrain.discourse.group/t/looking-for-the-best-way-to-organize-presentation-files-with-nextstrain-tutorials/2261)
**Author:** [@JozeRizel](https://nextstrain.discourse.group/u/JozeRizel)\ **Replies:** 0\ **Last updated:** [August 1, 2026, 7:33am UTC](https://nextstrain.discourse.group/t/looking-for-the-best-way-to-organize-presentation-files-with-nextstrain-tutorials/2261 "2026-08-01T07:33:01Z")
Hi everyone, I am new to Nextstrain and trying to learn from the official documentation and community posts. I also have some study presentations that I downloaded using a SlideShare Downloader, and I keep switching be… --- ## [SARS-CoV-2 workflow: nextclade.tsv.zst description](https://nextstrain.discourse.group/t/sars-cov-2-workflow-nextclade-tsv-zst-description/2255)
**Author:** [@mike\_honey](https://nextstrain.discourse.group/u/mike_honey)\ **Replies:** 3\ **Last updated:** [July 19, 2026, 7:03am UTC](https://nextstrain.discourse.group/t/sars-cov-2-workflow-nextclade-tsv-zst-description/2255 "2026-07-19T07:03:58Z")
The documentation page SARS-CoV-2 workflow \> Remote inputs mentions a file nextclade.tsv.zst which sounds intriguing. In my imagination, it is the output from processing all the sequences.fasta.zst output through the ne… --- ## [Auspice and auspice.us updates](https://nextstrain.discourse.group/t/auspice-and-auspice-us-updates/2259)
**Author:** [@nextstrain-team-bot](https://nextstrain.discourse.group/u/nextstrain-team-bot)\ **Replies:** 0\ **Last updated:** [July 9, 2026, 10:51pm UTC](https://nextstrain.discourse.group/t/auspice-and-auspice-us-updates/2259 "2026-07-09T22:51:38Z")
The Nextstrain team has been focused on extending the usability of Auspice and auspice.us. Here are a few features that we wanted to highlight: Offline use of auspice.us We have released a new version of auspice.us that… --- ## [How did you learn Nextstrain when starting from zero?](https://nextstrain.discourse.group/t/how-did-you-learn-nextstrain-when-starting-from-zero/2250)
**Author:** [@JozeRizel](https://nextstrain.discourse.group/u/JozeRizel)\ **Replies:** 1\ **Last updated:** [July 9, 2026, 5:24am UTC](https://nextstrain.discourse.group/t/how-did-you-learn-nextstrain-when-starting-from-zero/2250 "2026-07-09T05:24:18Z")
Hi everyone, I am new here and recently started exploring Nextstrain. I don’t have much experience with phylogenetics, so sometimes the documentation feels a little hard for me. I can follow some parts, but then I get … --- ## [SARS-CoV-2 - no entry in nightly build for RW.1.1.2?](https://nextstrain.discourse.group/t/sars-cov-2-no-entry-in-nightly-build-for-rw-1-1-2/2232)
**Author:** [@mike\_honey](https://nextstrain.discourse.group/u/mike_honey)\ **Replies:** 1\ **Last updated:** [July 4, 2026, 6:07am UTC](https://nextstrain.discourse.group/t/sars-cov-2-no-entry-in-nightly-build-for-rw-1-1-2/2232 "2026-07-04T06:07:14Z")
In the SARS-CoV-2 nightly build, I can see the new entries for RW.1.1.1 and RW.1.1.3, but RW.1.1.2 appears to be missing? I’m downloading from: https://nextstrain.org/charon/getDataset?prefix=staging/nextclade/sars-cov… --- ## [New location for discussion forum](https://nextstrain.discourse.group/t/new-location-for-discussion-forum/2237)
**Author:** [@victorlin](https://nextstrain.discourse.group/u/victorlin)\ **Replies:** 0\ **Last updated:** [June 24, 2026, 5:25pm UTC](https://nextstrain.discourse.group/t/new-location-for-discussion-forum/2237 "2026-06-24T17:25:40Z")
Our discussion forum has moved from discussion.nextstrain.org to nextstrain.discourse.group. You can continue to use your existing account at the new location. Old links will be automatically redirected. Please reply h… --- ## [Criteria for Selecting "Key Mutations" to Define Clades in Augur/Nextstrain](https://nextstrain.discourse.group/t/criteria-for-selecting-key-mutations-to-define-clades-in-augur-nextstrain/2164)
**Author:** [@hanguojun](https://nextstrain.discourse.group/u/hanguojun)\ **Replies:** 2\ **Last updated:** [June 24, 2026, 8:49am UTC](https://nextstrain.discourse.group/t/criteria-for-selecting-key-mutations-to-define-clades-in-augur-nextstrain/2164 "2026-06-24T08:49:54Z")
Hi, everyone I’m trying to generate a clade.tsv file to annotate specific clades in my tree.json. I know I can get mutation info by clicking/hovering on the tree as per the documentation, but I’m unsure about the criter… --- ## [Missing nucleotides in entropy output .tsv file](https://nextstrain.discourse.group/t/missing-nucleotides-in-entropy-output-tsv-file/2231)
**Author:** [@Keith](https://nextstrain.discourse.group/u/Keith)\ **Replies:** 1\ **Last updated:** [June 23, 2026, 12:00am UTC](https://nextstrain.discourse.group/t/missing-nucleotides-in-entropy-output-tsv-file/2231 "2026-06-23T00:00:09Z")
Hi, when I select for Dengue the whole genome, and export the genome diversity data (entropy) to a .tsv file, I have missing nucleotides in the output file. In my TSV file I only have 7947 rows for the genome that has 1… --- ## [Treetime dating - Negative branch lengths](https://nextstrain.discourse.group/t/treetime-dating-negative-branch-lengths/2045)
**Author:** [@georges.hanna](https://nextstrain.discourse.group/u/georges.hanna)\ **Replies:** 1\ **Last updated:** [May 25, 2026, 3:26pm UTC](https://nextstrain.discourse.group/t/treetime-dating-negative-branch-lengths/2045 "2026-05-25T15:26:45Z")
Hello everyone, I am trying to build a dated phylogenetic tree using TreeTime (version 0.12.1). I used the following command: treetime --tree tree.treefile --aln aln.fasta --dates dates.csv \\ --reconstruct-tip-stat… --- ## [SARS-CoV-2 - no PQ.16.1.1 calls?](https://nextstrain.discourse.group/t/sars-cov-2-no-pq-16-1-1-calls/2031)
**Author:** [@mike\_honey](https://nextstrain.discourse.group/u/mike_honey)\ **Replies:** 2\ **Last updated:** [May 25, 2026, 12:34am UTC](https://nextstrain.discourse.group/t/sars-cov-2-no-pq-16-1-1-calls/2031 "2026-05-25T00:34:54Z")
Yesterday I pushed the last few months of samples from GISAID through the latest Nextclade nightly build. I got 16 samples of PQ.16.1, but none at all of PQ.16.1.1. Is there some issue with it at your end? --- ## [Plot augur refine tree with ggtree](https://nextstrain.discourse.group/t/plot-augur-refine-tree-with-ggtree/2017)
**Author:** [@diegogotex](https://nextstrain.discourse.group/u/diegogotex)\ **Replies:** 2\ **Last updated:** [March 24, 2026, 10:31am UTC](https://nextstrain.discourse.group/t/plot-augur-refine-tree-with-ggtree/2017 "2026-03-24T10:31:38Z")
Hi all, I’ve been trying to plot the calibrated tree from Augur Refine using GGTree in R, but the scale on the x-axis doesn’t match that on the Auspice visualisation. I ran augur-refine with the following command: aug… --- ## [PRRSV1 Reference Dataset](https://nextstrain.discourse.group/t/prrsv1-reference-dataset/2025)
**Author:** [@ngoctiep](https://nextstrain.discourse.group/u/ngoctiep)\ **Replies:** 1\ **Last updated:** [March 9, 2026, 6:26pm UTC](https://nextstrain.discourse.group/t/prrsv1-reference-dataset/2025 "2026-03-09T18:26:48Z")
Hello, Where can I download the PRRSV1 dataset? The one on GitHub only has one strain. --- ## [Include external tools in the Nextstrain Snakemake workflow](https://nextstrain.discourse.group/t/include-external-tools-in-the-nextstrain-snakemake-workflow/2021)
**Author:** [@jonr](https://nextstrain.discourse.group/u/jonr)\ **Replies:** 3\ **Last updated:** [February 6, 2026, 5:58pm UTC](https://nextstrain.discourse.group/t/include-external-tools-in-the-nextstrain-snakemake-workflow/2021 "2026-02-06T17:58:03Z")
Hi, I’m using the nextstrain build Docker-based workflow. And I want to include the tool “Treemmer” to reduce a phylogenetic tree afte the initial “augur tree”. Treemmer can be installed locally, but is also available a… --- ## [How to get the correct time axis when using augur refine and timetree?](https://nextstrain.discourse.group/t/how-to-get-the-correct-time-axis-when-using-augur-refine-and-timetree/2020)
**Author:** [@jonr](https://nextstrain.discourse.group/u/jonr)\ **Replies:** 4\ **Last updated:** [February 4, 2026, 9:18pm UTC](https://nextstrain.discourse.group/t/how-to-get-the-correct-time-axis-when-using-augur-refine-and-timetree/2020 "2026-02-04T21:18:11Z")
Hi, I’m running this command: Shell command: augur refine --tree nextstrain\_results/tree\_raw.nwk --alignment nextstrain\_results/aligned.fasta --metadata phylogeny/genotypes\_combined… --- ## [SSL error when trying to push Json files to our private group APHA-H5Nx-Avian-Influenza using conda](https://nextstrain.discourse.group/t/ssl-error-when-trying-to-push-json-files-to-our-private-group-apha-h5nx-avian-influenza-using-conda/2018)
**Author:** [@BenAPHA](https://nextstrain.discourse.group/u/BenAPHA)\ **Replies:** 4\ **Last updated:** [February 2, 2026, 8:50pm UTC](https://nextstrain.discourse.group/t/ssl-error-when-trying-to-push-json-files-to-our-private-group-apha-h5nx-avian-influenza-using-conda/2018 "2026-02-02T20:50:47Z")
When trying to push Auspice json files to out private Nextstrain group: APHA-H5Nx-Avian-Influenza but run into this error: ‘\[SSL: CERTIFICATE\_VERIFY\_FAILED\] certificate verify failed: Missing Authority Key Identifier (… --- ## [Hosting build on github](https://nextstrain.discourse.group/t/hosting-build-on-github/2019)
**Author:** [@rtk](https://nextstrain.discourse.group/u/rtk)\ **Replies:** 1\ **Last updated:** [January 28, 2026, 7:42pm UTC](https://nextstrain.discourse.group/t/hosting-build-on-github/2019 "2026-01-28T19:42:05Z")
I am trying to host my build from my github where all I have is the build in a folder called auspice. However https://nextstrain.org/community/rtobiaskoch/csuwnvpublic is yielding no results. I have managed to host bu… --- ## [Incorperating \`argur distance\` outputs](https://nextstrain.discourse.group/t/incorperating-argur-distance-outputs/1265)
**Author:** [@ellisrichardj](https://nextstrain.discourse.group/u/ellisrichardj)\ **Replies:** 6\ **Last updated:** [January 21, 2026, 7:22pm UTC](https://nextstrain.discourse.group/t/incorperating-argur-distance-outputs/1265 "2026-01-21T19:22:16Z")
Hi I have been using augur distance to generate a distance matrix for my data using the --compare-to pairwise argument. This is producing a sensible .json output. What I haven’t been able to work out is how to incorpo… --- ## [Nextclade short clade annotation H1N1](https://nextstrain.discourse.group/t/nextclade-short-clade-annotation-h1n1/2016)
**Author:** [@georges.hanna](https://nextstrain.discourse.group/u/georges.hanna)\ **Replies:** 1\ **Last updated:** [January 15, 2026, 9:15pm UTC](https://nextstrain.discourse.group/t/nextclade-short-clade-annotation-h1n1/2016 "2026-01-15T21:15:29Z")
Hello, I am trying to annotate H1N1 sequences uysing nextclade web version and the ref dataset of 2019, but when I download the tsv output annotation file, I cannot find columns for short clade and legacy-clade. The onl… --- ## [How to set up next strain](https://nextstrain.discourse.group/t/how-to-set-up-next-strain/2011)
**Author:** [@N\_MBERS](https://nextstrain.discourse.group/u/N_MBERS)\ **Replies:** 2\ **Last updated:** [January 8, 2026, 7:17pm UTC](https://nextstrain.discourse.group/t/how-to-set-up-next-strain/2011 "2026-01-08T19:17:37Z")
Hii this is Kelvin from the last meeting just wanted to know how to set up nextstrain tool --- ## [Nextstrain phylogenetic tree in the format used by UCSC](https://nextstrain.discourse.group/t/nextstrain-phylogenetic-tree-in-the-format-used-by-ucsc/1707)
**Author:** [@sunbrn](https://nextstrain.discourse.group/u/sunbrn)\ **Replies:** 9\ **Last updated:** [December 16, 2025, 10:43pm UTC](https://nextstrain.discourse.group/t/nextstrain-phylogenetic-tree-in-the-format-used-by-ucsc/1707 "2025-12-16T22:43:51Z")
Is there a downloadable version of the SARS-CoV-2 Nextstrain phylogenetic tree (from GISAID data) with the same (or similar) format to the one used by UCSC (here: kent/src/hg/utils/otto/sarscov2phylo/pango.clade-mutation… --- ## [How do we establish a private mutation threshold for new datasets?](https://nextstrain.discourse.group/t/how-do-we-establish-a-private-mutation-threshold-for-new-datasets/2006)
**Author:** [@fdezordi](https://nextstrain.discourse.group/u/fdezordi)\ **Replies:** 2\ **Last updated:** [December 8, 2025, 1:12pm UTC](https://nextstrain.discourse.group/t/how-do-we-establish-a-private-mutation-threshold-for-new-datasets/2006 "2025-12-08T13:12:59Z")
Hi everyone, I’m currently testing the creation of Nextclade datasets for some viruses, and I’m trying to understand how to choose appropriate values for the typical and cutoff fields in the privateMutations QC section … --- ## [Reference Dataset](https://nextstrain.discourse.group/t/reference-dataset/2005)
**Author:** [@eli\_rdp](https://nextstrain.discourse.group/u/eli_rdp)\ **Replies:** 1\ **Last updated:** [November 10, 2025, 8:37pm UTC](https://nextstrain.discourse.group/t/reference-dataset/2005 "2025-11-10T20:37:47Z")
Hello. I have been using Nextclade web to analyze my RSV data. I usually used the reference listed in the metadata, which I downloaded from auspice web. I noticed there is a change in the accession listed in the metadat… --- ## [Entire recent SARS-CoV-2 batch from Cote d’Ivoire not output from Nextclade CLI](https://nextstrain.discourse.group/t/entire-recent-sars-cov-2-batch-from-cote-d-ivoire-not-output-from-nextclade-cli/2004)
**Author:** [@mike\_honey](https://nextstrain.discourse.group/u/mike_honey)\ **Replies:** 4\ **Last updated:** [November 6, 2025, 10:43am UTC](https://nextstrain.discourse.group/t/entire-recent-sars-cov-2-batch-from-cote-d-ivoire-not-output-from-nextclade-cli/2004 "2025-11-06T10:43:47Z")
I was just refreshing my data from GISAID and I noticed the entire recent batch of 65 samples from Cote d’Ivoire did not appear in the output-tsv produced from the Nextclade CLI. There were no messages produced. For exa… --- ## [Recent comparison of nextclade and pangolin](https://nextstrain.discourse.group/t/recent-comparison-of-nextclade-and-pangolin/2003)
**Author:** [@adalisan](https://nextstrain.discourse.group/u/adalisan)\ **Replies:** 1\ **Last updated:** [November 4, 2025, 10:48pm UTC](https://nextstrain.discourse.group/t/recent-comparison-of-nextclade-and-pangolin/2003 "2025-11-04T22:48:13Z")
For Pango lineage assignments for SARS-COV2 sequences, is there a more recent comparison between nextclade and Pangolearn or Usher-based pangolin assignments? The description here is very useful, but relevant for data f… --- ## [Filter for create Dengue phylogenetic tree](https://nextstrain.discourse.group/t/filter-for-create-dengue-phylogenetic-tree/1995)
**Author:** [@Soon\_tare](https://nextstrain.discourse.group/u/Soon_tare)\ **Replies:** 7\ **Last updated:** [November 3, 2025, 8:22am UTC](https://nextstrain.discourse.group/t/filter-for-create-dengue-phylogenetic-tree/1995 "2025-11-03T08:22:44Z")
Hello, Nextstrain developer, I have a question to ask you about the filter for creating dengue phylogenetics. When I attempt to filter all sequences from my local sample to display on the dengue phylogenetic tree, I find… --- ## [Measles root sequence](https://nextstrain.discourse.group/t/measles-root-sequence/1693)
**Author:** [@roberthohan](https://nextstrain.discourse.group/u/roberthohan)\ **Replies:** 5\ **Last updated:** [October 29, 2025, 10:36pm UTC](https://nextstrain.discourse.group/t/measles-root-sequence/1693 "2025-10-29T22:36:56Z")
Simple question: for determining the mutations in full genome measles sequences, which strain is used as the reference (root)? As far as I can tell so far it is one that is subtype A, but I’d like to know the precise acc… [Next page](https://nextstrain.discourse.group/latest.md?page=1)