Help and Getting Started

Topic	Replies	Views	Activity
About the Help and Getting Started category Whether you’re just getting started or a seasoned expert, this is the place to troubleshoot problems, debug workflows, and puzzle over analyses. If you need or can offer help with Nextstrain, make a new topic in this cat…	2	949	June 19, 2020
Reference Dataset	1	18	November 10, 2025
Entire recent SARS-CoV-2 batch from Cote d’Ivoire not output from Nextclade CLI	4	41	November 6, 2025
Filter for create Dengue phylogenetic tree	7	82	November 3, 2025
Measles root sequence	5	95	October 29, 2025
Building custom nextclade dataset norovirus	7	57	October 17, 2025
Error when trying to download zika pathogen repository	1	25	October 14, 2025
Teacher Q on Nextclade RSV-A reference dataset	5	46	October 2, 2025
Requested color-by field 'num_date' does not exist	3	38	September 25, 2025
Consensus on how to deal with segmented viruses?	5	66	September 22, 2025
Metadata.tsv: building custom nextclade dataset	3	65	August 20, 2025
Accessing geospatial data to map where and when a virus is most common	1	35	August 13, 2025
Xz: command not found	5	79	August 13, 2025
Why the zika tree doesn't include African genotype?	0	23	August 13, 2025
The pipeline takes a very long time to complete	14	104	August 11, 2025
How can I know what columns will be in nextclade output?	11	99	August 5, 2025
Updated Runtime - unable to update CLI and view results	3	42	August 4, 2025
Phylogenetic tree and map of plant viruses	1	54	July 30, 2025
How to display the distribution of lineages on a world map in auspice using the nextstrain build pipeline?	3	58	July 30, 2025
Use the pre-built phylogenetic trees for further analysis	0	45	July 8, 2025
Strain ID and the tab-delimited metadata in Prepare the Sequences	4	61	June 23, 2025
Sequecing data for Africa-Nigeria-Bayelsa	0	27	June 11, 2025
How to use criteria to use data from database (Genbank & GISAID)	0	39	June 11, 2025
Data displayed on nexstrain.org vs downloadable data	2	46	June 5, 2025
Mapbox display issue (api changing without building auspice)	3	52	May 12, 2025
How do I install additional packages in the nextstrain conda environment?	2	58	April 17, 2025
Customizing Colors in Nextstrain SARS-CoV-2 Temporal Phylogenetic Tree for Enhanced Analysis	5	90	March 31, 2025
SARS-CoV-2 new lineage BA.3.2 still not in nightly.json	2	154	March 29, 2025
Tree visualization issue with num_date	1	44	March 24, 2025
Using influenza datasets in clades.nextstrain.org	7	124	March 20, 2025

About the Help and Getting Started category

Whether you’re just getting started or a seasoned expert, this is the place to troubleshoot problems, debug workflows, and puzzle over analyses. If you need or can offer help with Nextstrain, make a new topic in this cat…