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	936	June 19, 2020
How to display the distribution of lineages on a world map in auspice using the nextstrain build pipeline?	1	4	July 25, 2025
How can I know what columns will be in nextclade output?	10	34	July 24, 2025
Use the pre-built phylogenetic trees for further analysis	0	18	July 8, 2025
Strain ID and the tab-delimited metadata in Prepare the Sequences	4	35	June 23, 2025
Sequecing data for Africa-Nigeria-Bayelsa	0	7	June 11, 2025
How to use criteria to use data from database (Genbank & GISAID)	0	14	June 11, 2025
Data displayed on nexstrain.org vs downloadable data	2	20	June 5, 2025
Mapbox display issue (api changing without building auspice)	3	29	May 12, 2025
How do I install additional packages in the nextstrain conda environment?	2	42	April 17, 2025
Customizing Colors in Nextstrain SARS-CoV-2 Temporal Phylogenetic Tree for Enhanced Analysis	5	55	March 31, 2025
SARS-CoV-2 new lineage BA.3.2 still not in nightly.json	2	102	March 29, 2025
Tree visualization issue with num_date	1	24	March 24, 2025
Using influenza datasets in clades.nextstrain.org	7	70	March 20, 2025
Phylogeny analysis of RSV A and B	0	49	February 18, 2025
Using marginal for augur traits	0	24	February 14, 2025
Trouble with SARS_CoV_2	38	122	February 10, 2025
Where can I look up clade defining mutations for seasonal flu?	1	463	February 4, 2025
Is it possible to display the "Second Tree" dropdown menu in a Nextstrain group?	2	17	January 30, 2025
Nextclade CLI error - Alignment matrix size exceeds maximum value	2	37	January 14, 2025
Displaying a Map in Auspice	5	463	January 5, 2025
New version rule align error	2	29	December 29, 2024
I want to make a phylogenetic tree using augur and auspice pipeline that analyzes the transmission of SARS-CoV-2 from the global context into the Philippines	0	19	December 28, 2024
Timing of nightly build	2	27	December 24, 2024
Problems with coordinate binding	2	22	November 23, 2024
Nextstrain files/datasets in Google Cloud (GCP)?	3	30	November 22, 2024
Load json fails when change dataset on nextstrain	1	15	November 20, 2024
Error: Alignment must have at least 3 sequences	9	1042	November 7, 2024
RSV-A lineage reference sequences have discordant clade assignments	3	60	October 27, 2024
Nextclade set of possible lineages or distance metric	2	44	October 6, 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…