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	937	June 19, 2020
Consensus on how to deal with segmented viruses?	3	30	September 12, 2025
Metadata.tsv: building custom nextclade dataset	3	38	August 20, 2025
Accessing geospatial data to map where and when a virus is most common	1	22	August 13, 2025
Xz: command not found	5	37	August 13, 2025
Why the zika tree doesn't include African genotype?	0	14	August 13, 2025
The pipeline takes a very long time to complete	14	83	August 11, 2025
How can I know what columns will be in nextclade output?	11	69	August 5, 2025
Updated Runtime - unable to update CLI and view results	3	21	August 4, 2025
Phylogenetic tree and map of plant viruses	1	33	July 30, 2025
How to display the distribution of lineages on a world map in auspice using the nextstrain build pipeline?	3	35	July 30, 2025
Use the pre-built phylogenetic trees for further analysis	0	27	July 8, 2025
Strain ID and the tab-delimited metadata in Prepare the Sequences	4	40	June 23, 2025
Sequecing data for Africa-Nigeria-Bayelsa	0	12	June 11, 2025
How to use criteria to use data from database (Genbank & GISAID)	0	19	June 11, 2025
Data displayed on nexstrain.org vs downloadable data	2	26	June 5, 2025
Mapbox display issue (api changing without building auspice)	3	39	May 12, 2025
How do I install additional packages in the nextstrain conda environment?	2	45	April 17, 2025
Customizing Colors in Nextstrain SARS-CoV-2 Temporal Phylogenetic Tree for Enhanced Analysis	5	60	March 31, 2025
SARS-CoV-2 new lineage BA.3.2 still not in nightly.json	2	115	March 29, 2025
Tree visualization issue with num_date	1	27	March 24, 2025
Using influenza datasets in clades.nextstrain.org	7	84	March 20, 2025
Phylogeny analysis of RSV A and B	0	53	February 18, 2025
Using marginal for augur traits	0	29	February 14, 2025
Trouble with SARS_CoV_2	38	164	February 10, 2025
Where can I look up clade defining mutations for seasonal flu?	1	466	February 4, 2025
Is it possible to display the "Second Tree" dropdown menu in a Nextstrain group?	2	21	January 30, 2025
Nextclade CLI error - Alignment matrix size exceeds maximum value	2	39	January 14, 2025
Displaying a Map in Auspice	5	486	January 5, 2025
New version rule align error	2	33	December 29, 2024

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…