Running discrete phylogeographies on large datasets
Link to full SOP: https://docs.google.com/document/d/1mTwKrQ6UCP75_5ncyiS2RjE4tdn5LJOTCve_cbH0j7c/edit#
Credit for thorney beast method: Dr JT McCrone
- Get ML topology with IQTree
iqtree -fast -m hky -s alignment.fasta -nt AUTO -o outgroup.taxon -czb
1b. Prune outgroup
jclusterfunk prune -i <input_file> -taxa <id> -output <output_file>
- Scale roughly in time with Treetime (optional but recommended for runtime efficiency)
treetime --sequence-length <length_of_alignment> --tree <input.nwk> --dates <dates.csv> --keep-root
- Scale properly in time with thorney beast
Use thorney_beast.xml as a template
3b. Grab last tree from that file
X = 2n+9 where n is the number of taxa BUT I recommmend checking it - it seems that it varies a bit
[on Command line]
head -X trees_file.tree > top_section.txt
tail -2 trees_file.tree > last_tree.txt
cat top_section.txt last_tree.txt > best_tree.txt
- Run DTA Use DTA_template.xml as a template