# General **URL:** https://nextstrain.discourse.group/c/general/5.md [Latest](https://nextstrain.discourse.group/latest.md) · [Categories](https://nextstrain.discourse.group/categories.md) --- ## [About the General category](https://nextstrain.discourse.group/t/about-the-general-category/31)
**Author:** [@trs](https://nextstrain.discourse.group/u/trs)\ **Replies:** 0\ **Last updated:** [June 19, 2020, 5:02pm UTC](https://nextstrain.discourse.group/t/about-the-general-category/31 "2020-06-19T17:02:15Z")
This category is for general discussion about anything and everything Nextstrain. Make a new topic in this category to: Describe how you’re currently using Nextstrain, so everyone can see awesome examples of genomic … --- ## [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… --- ## [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… --- ## [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… --- ## [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… --- ## [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. --- ## [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 … --- ## [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… --- ## [Query about M2-2 gene annotation discrepancy in Nextstrain RSV-A module](https://nextstrain.discourse.group/t/query-about-m2-2-gene-annotation-discrepancy-in-nextstrain-rsv-a-module/1962)
**Author:** [@yangjq](https://nextstrain.discourse.group/u/yangjq)\ **Replies:** 3\ **Last updated:** [September 28, 2025, 8:33am UTC](https://nextstrain.discourse.group/t/query-about-m2-2-gene-annotation-discrepancy-in-nextstrain-rsv-a-module/1962 "2025-09-28T08:33:42Z")
Dear Nextstrain Team, I hope this message finds you well. I am writing to seek clarification regarding the annotation of the M2-2 gene in the RSV-A module on Nextstrain. I noticed a discrepancy between the M2-2 gene co… --- ## [Filter parameters for all-time global SARS-CoV-2 dataset](https://nextstrain.discourse.group/t/filter-parameters-for-all-time-global-sars-cov-2-dataset/1992)
**Author:** [@diegogotex](https://nextstrain.discourse.group/u/diegogotex)\ **Replies:** 2\ **Last updated:** [August 22, 2025, 11:10am UTC](https://nextstrain.discourse.group/t/filter-parameters-for-all-time-global-sars-cov-2-dataset/1992 "2025-08-22T11:10:03Z")
Hi all, I’m using the SARS-CoV-2 all-time global dataset ( auspice ) to generate a small tree by adding some new samples. Is there any documentation available about the filters that are applied to generate the sets for… --- ## [Chikungunya Virus, 250 years old?](https://nextstrain.discourse.group/t/chikungunya-virus-250-years-old/1967)
**Author:** [@jiehuang001](https://nextstrain.discourse.group/u/jiehuang001)\ **Replies:** 3\ **Last updated:** [August 10, 2025, 6:39pm UTC](https://nextstrain.discourse.group/t/chikungunya-virus-250-years-old/1967 "2025-08-10T18:39:00Z")
Hi, there: I downloaded the high-depth sequence data for 4,590 Chikungunya Virus from GISAID, and run a nextstrain analysis. Please see the screenshot below. I am so surprised to see that the inferred root of the phylog… --- ## [Negative Dates in Auspice Timeline When Using YY-XX-XX Format](https://nextstrain.discourse.group/t/negative-dates-in-auspice-timeline-when-using-yy-xx-xx-format/1964)
**Author:** [@Komal](https://nextstrain.discourse.group/u/Komal)\ **Replies:** 1\ **Last updated:** [August 4, 2025, 6:46pm UTC](https://nextstrain.discourse.group/t/negative-dates-in-auspice-timeline-when-using-yy-xx-xx-format/1964 "2025-08-04T18:46:08Z")
Hi, I’m encountering an issue where the Auspice timeline displays large negative date values (e.g., -89900). In my metadata file, the date column is formatted as YY-XX-XX - for example, 26-XX-XX for the year 2026 with u… --- ## [Inconsistent QC Results Between Nextclade CLI and Web Version](https://nextstrain.discourse.group/t/inconsistent-qc-results-between-nextclade-cli-and-web-version/1966)
**Author:** [@georges.hanna](https://nextstrain.discourse.group/u/georges.hanna)\ **Replies:** 2\ **Last updated:** [August 4, 2025, 11:49am UTC](https://nextstrain.discourse.group/t/inconsistent-qc-results-between-nextclade-cli-and-web-version/1966 "2025-08-04T11:49:37Z")
Hello everyone, I’m working with a SARS-CoV-2 dataset and trying to filter sequences based on qc.overallStatus using Nextclade. When I run Nextclade via the command line, all my sequences are labeled with “good” qualit… --- ## [H1N1 pdm09 tree - EPI ISL identifiers](https://nextstrain.discourse.group/t/h1n1-pdm09-tree-epi-isl-identifiers/1921)
**Author:** [@georges.hanna](https://nextstrain.discourse.group/u/georges.hanna)\ **Replies:** 1\ **Last updated:** [June 26, 2025, 11:04pm UTC](https://nextstrain.discourse.group/t/h1n1-pdm09-tree-epi-isl-identifiers/1921 "2025-06-26T23:04:45Z")
I’m trying to download the acknowledgments for the H1N1pdm09 (seasonal influenza) dataset from Nextstrain. However, I can only see the virus names — the EPI\_ISL identifiers for the sequences are not available. I need to … --- ## [Need new reference sequences for SARS-CoV2?](https://nextstrain.discourse.group/t/need-new-reference-sequences-for-sars-cov2/1896)
**Author:** [@LPI](https://nextstrain.discourse.group/u/LPI)\ **Replies:** 1\ **Last updated:** [June 15, 2025, 5:16pm UTC](https://nextstrain.discourse.group/t/need-new-reference-sequences-for-sars-cov2/1896 "2025-06-15T17:16:03Z")
Hello, It’s been a while since I last used Nextclade, and a majority of the sequences I’ve submitted for samples taken between January and April 2025 show a very high number of mutations. The reference sequence used is … --- ## [RSV-A Reference Sequence Question](https://nextstrain.discourse.group/t/rsv-a-reference-sequence-question/1908)
**Author:** [@T4R4](https://nextstrain.discourse.group/u/T4R4)\ **Replies:** 2\ **Last updated:** [June 13, 2025, 2:20pm UTC](https://nextstrain.discourse.group/t/rsv-a-reference-sequence-question/1908 "2025-06-13T14:20:10Z")
Hello, I noticed that the referenced RSV-A NCBI accession has been updated to the INSDC reference that differs slightly from the A/England/397/2017 reference used in the RSV-A Nextclade dataset. I was wondering if there… --- ## [Output all amino acids per CDS using Nextclade](https://nextstrain.discourse.group/t/output-all-amino-acids-per-cds-using-nextclade/1889)
**Author:** [@jonr](https://nextstrain.discourse.group/u/jonr)\ **Replies:** 2\ **Last updated:** [May 7, 2025, 7:04am UTC](https://nextstrain.discourse.group/t/output-all-amino-acids-per-cds-using-nextclade/1889 "2025-05-07T07:04:33Z")
Hi, For Hepatitis C Virus some of the wildtype aa residues give resistance to certain drugs. I am therefore interested in making a list of all the residues at all positions of the CDS in the gff3 file, not only the diff… --- ## [Downloading mpox fasta files](https://nextstrain.discourse.group/t/downloading-mpox-fasta-files/1885)
**Author:** [@ndimenstein](https://nextstrain.discourse.group/u/ndimenstein)\ **Replies:** 1\ **Last updated:** [April 17, 2025, 7:05pm UTC](https://nextstrain.discourse.group/t/downloading-mpox-fasta-files/1885 "2025-04-17T19:05:39Z")
Is it possible to download the mpox sequences displayed on the phylogenetic trees as raw fasta files? Thank you, Netanel --- ## [Are there any other groups working on Orthonairovirus haemorrhagiae typing](https://nextstrain.discourse.group/t/are-there-any-other-groups-working-on-orthonairovirus-haemorrhagiae-typing/1876)
**Author:** [@birdj1](https://nextstrain.discourse.group/u/birdj1)\ **Replies:** 0\ **Last updated:** [March 27, 2025, 1:23pm UTC](https://nextstrain.discourse.group/t/are-there-any-other-groups-working-on-orthonairovirus-haemorrhagiae-typing/1876 "2025-03-27T13:23:55Z")
Our group is working on a strain typing project for Orthonairovirus haemorrhagiae (CCHVF). We would love to utilize the tools and community that are here at Nextstrain as much as possible. I am curious if there are alrea… --- ## [Serving Asupice with NGINX](https://nextstrain.discourse.group/t/serving-asupice-with-nginx/1863)
**Author:** [@mhananda](https://nextstrain.discourse.group/u/mhananda)\ **Replies:** 6\ **Last updated:** [March 24, 2025, 4:14pm UTC](https://nextstrain.discourse.group/t/serving-asupice-with-nginx/1863 "2025-03-24T16:14:17Z")
Hi I would like to know how i can display the auspice tree in my website via iframe? I am trying to use nginx with this config for location /auspice { proxy\_pass http://127.0.0.1:4000/auspice; proxy\_htt… --- ## [File traitsdivision.mugration\_model](https://nextstrain.discourse.group/t/file-traitsdivision-mugration-model/1210)
**Author:** [@juan\_dc](https://nextstrain.discourse.group/u/juan_dc)\ **Replies:** 4\ **Last updated:** [March 21, 2025, 12:15pm UTC](https://nextstrain.discourse.group/t/file-traitsdivision-mugration-model/1210 "2025-03-21T12:15:42Z")
Hello, checking the files in the results folder I found the file traitsdivision.mugration\_model.txt I have searched how to understand these tables but I can’t find anything in the forum, can someone help me to interpret… --- ## [Using marginal likelihood with augur](https://nextstrain.discourse.group/t/using-marginal-likelihood-with-augur/1868)
**Author:** [@aguang](https://nextstrain.discourse.group/u/aguang)\ **Replies:** 0\ **Last updated:** [March 12, 2025, 2:42pm UTC](https://nextstrain.discourse.group/t/using-marginal-likelihood-with-augur/1868 "2025-03-12T14:42:02Z")
I posted this in Getting Started a while ago but it seems like General is the topic that actually gets traffic. It’s my understanding that ancestral reconstruction is done with maximum likelihood methods, I can see there… --- ## [Build with newest nextstrain/ncov has API requests to mapbox 403:Forbidden](https://nextstrain.discourse.group/t/build-with-newest-nextstrain-ncov-has-api-requests-to-mapbox-403-forbidden/396)
**Author:** [@rsultana](https://nextstrain.discourse.group/u/rsultana)\ **Replies:** 15\ **Last updated:** [February 13, 2025, 5:41pm UTC](https://nextstrain.discourse.group/t/build-with-newest-nextstrain-ncov-has-api-requests-to-mapbox-403-forbidden/396 "2025-02-13T17:41:30Z")
Hi! I have made a few custom local builds (for the samples we have in Hawaii) using the latest commit of nextstrain/ncov because of the wonderful frequencies panel that I wanted to add to our builds. I managed to get … --- ## [New clade/lineage/sublineage criteria for mpox](https://nextstrain.discourse.group/t/new-clade-lineage-sublineage-criteria-for-mpox/1812)
**Author:** [@pehenriquejp](https://nextstrain.discourse.group/u/pehenriquejp)\ **Replies:** 3\ **Last updated:** [January 15, 2025, 11:56pm UTC](https://nextstrain.discourse.group/t/new-clade-lineage-sublineage-criteria-for-mpox/1812 "2025-01-15T23:56:22Z")
Hi everyone, I would like to know what criteria are used in Nextstrain to define a new clade, lineage, or sublineage for mpox. I reviewed the literature and documentation and found some information for SARS-CoV-2 (examp… --- ## [IDs of early delta-like strains](https://nextstrain.discourse.group/t/ids-of-early-delta-like-strains/1786)
**Author:** [@hyanwong](https://nextstrain.discourse.group/u/hyanwong)\ **Replies:** 0\ **Last updated:** [November 25, 2024, 2:51pm UTC](https://nextstrain.discourse.group/t/ids-of-early-delta-like-strains/1786 "2024-11-25T14:51:31Z")
I’m looking for sample strains that are similar to the purported origin of the Delta SARS-CoV2 wave. I know that some stains suffer from wrongly associated dates, so I don’t want to just take the earliest B.1.617.2 strai… --- ## [Web App and Nextclade (Pango)](https://nextstrain.discourse.group/t/web-app-and-nextclade-pango/1768)
**Author:** [@ABissonn](https://nextstrain.discourse.group/u/ABissonn)\ **Replies:** 1\ **Last updated:** [November 1, 2024, 7:54pm UTC](https://nextstrain.discourse.group/t/web-app-and-nextclade-pango/1768 "2024-11-01T19:54:59Z")
Hello, I am a research specialist at the Marshfield Clinic Research Institute, and I have previously used the Nextclade web app for Flu and SARS-CoV-2 lineage reports. Recently, I noticed our SARS-CoV-2 bioinformatics a… --- ## [Fix\_tree.py error for mpox trees](https://nextstrain.discourse.group/t/fix-tree-py-error-for-mpox-trees/1762)
**Author:** [@dlu](https://nextstrain.discourse.group/u/dlu)\ **Replies:** 3\ **Last updated:** [October 28, 2024, 6:04pm UTC](https://nextstrain.discourse.group/t/fix-tree-py-error-for-mpox-trees/1762 "2024-10-28T18:04:44Z")
In the step python3 scripts/fix\_tree.py --alignment results/aspen/masked.fasta --input-tree results/aspen/tree\_raw.nwk --output results/aspen/tree\_fixed.nwk For some … --- ## [Nextstrain Installation](https://nextstrain.discourse.group/t/nextstrain-installation/1757)
**Author:** [@NikitaSitharam](https://nextstrain.discourse.group/u/NikitaSitharam)\ **Replies:** 8\ **Last updated:** [October 22, 2024, 5:07pm UTC](https://nextstrain.discourse.group/t/nextstrain-installation/1757 "2024-10-22T17:07:08Z")
Hi Nextstrain Team, I have been running workflows using the Nextstrain CLI for the last 3 months. However, today I tried to run a workflow but keep getting this error: Traceback (most recent call last): File "/Users… [Next page](https://nextstrain.discourse.group/c/general/5.md?page=1)