methods_description.Rmd

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## Nextstrain methods

An interactive web-based visualization of SCYLV genomes was made using the Nextstrain pipeline [@hadfield2018nextstrain].
The main steps of the pipeline are summarized here.
A multiple sequence alignment of the genomes was made using `mafft` v7.475 with the FFT-NS-2 method [@katoh2005mafft].
A maximum likelihood tree was inferred from the multiple sequence alignment using `iqtree` v2.1.2 [@minh2020iq]
The `augur refine` command was used to create a timetree by estimating a molecular clock and rerooting the maximum likelihood tree using TreeTime v0.8.5 [@sagulenko2018treetime].
Tips of the tree were removed if their divergence vs. time correlation deviated more than 10 times the interquartile range of all samples.
Ancestral sequences and geographic locations were inferred using the `augur ancestral` and `augur traits` commands respectively.
The results of the pipeline were visualized using `auspice` [@hadfield2018nextstrain].
The code for the analysis is available at https://github.com/grunwaldlab/scylv and the interactive output of is hosted at https://nextstrain.org/community/grunwaldlab/scylv.