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	931	June 19, 2020
Mapbox display issue (api changing without building auspice)	3	13	May 12, 2025
How do I install additional packages in the nextstrain conda environment?	2	33	April 17, 2025
Customizing Colors in Nextstrain SARS-CoV-2 Temporal Phylogenetic Tree for Enhanced Analysis	5	51	March 31, 2025
SARS-CoV-2 new lineage BA.3.2 still not in nightly.json	2	74	March 29, 2025
Tree visualization issue with num_date	1	19	March 24, 2025
Using influenza datasets in clades.nextstrain.org	7	61	March 20, 2025
Phylogeny analysis of RSV A and B	0	43	February 18, 2025
Using marginal for augur traits	0	21	February 14, 2025
Trouble with SARS_CoV_2	38	94	February 10, 2025
Where can I look up clade defining mutations for seasonal flu?	1	455	February 4, 2025
Is it possible to display the "Second Tree" dropdown menu in a Nextstrain group?	2	14	January 30, 2025
Nextclade CLI error - Alignment matrix size exceeds maximum value	2	29	January 14, 2025
Displaying a Map in Auspice	5	452	January 5, 2025
New version rule align error	2	27	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	25	December 24, 2024
Problems with coordinate binding	2	20	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	1030	November 7, 2024
RSV-A lineage reference sequences have discordant clade assignments	3	50	October 27, 2024
Nextclade set of possible lineages or distance metric	2	35	October 6, 2024
Are gaps due to true insertions ok to leave in the alignment?	1	44	August 20, 2024
View in NextClade Feature	0	19	September 20, 2024
Tree shows an X at the end of branches... what do they mean?	2	57	July 22, 2024
Difference between sequence samples based on Dataset	1	31	September 16, 2024
Mpox Sequence Changes from Root	2	57	September 5, 2024
"Could not determine delimiter" error with metadata files	5	179	August 28, 2024
Influenza vaccine selection dates	1	23	August 15, 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…