This repository contains two workflows for the analysis of mammalian cytochrome b sequences:

• ingest/ - Download cytochrome b sequences from GenBank across all mammals
• phylogenetic/ - Filter sequences, align, construct phylogeny and export for visualization

Each folder contains a README.md with more information.

Follow the standard installation instructions for Nextstrain's suite of software tools.

First, fetch cytochrome b sequences from GenBank:

cd ingest
nextstrain build .

Then, build the phylogenetic tree:

cd ../phylogenetic
cp ../ingest/results/sequences.fasta data/
cp ../ingest/results/metadata.tsv data/
nextstrain build .
nextstrain view .

• Running a pathogen workflow
• Contributor documentation