Tutorial

Files used are in the examples folder.

curl -LO https://raw.githubusercontent.com/jonchang/tact/HEAD/examples/Carangaria.csv
curl -LO https://raw.githubusercontent.com/jonchang/tact/HEAD/examples/Carangaria.tre

Build a taxonomic tree using the provided CSV file. Run tact_build_taxonomic_tree --help to see the required format for this file.

$ tact_build_taxonomic_tree Carangaria.csv --output Carangaria.taxonomy.tre
Output written to: Carangaria.taxonomy.tre

Carangaria.taxonomy.tre now contains a Newick phylogeny with many polytomies and named nodes indicating relevant taxonomic ranks. Now run the TACT stochastic polytomy resolver algorithm in conjunction with the backbone phylogeny Caragaria.tre.

$ tact_add_taxa --backbone Carangaria.tre --taxonomy Carangaria.taxonomy.tre --output Carangaria.tacted --verbose --verbose
Rates  [####################################]  226/226
TACT  [####################################]  642/642  Carangaria

There will be several files created with the prefix Carangaria.tacted. These include newick.tre and nexus.tre (your primary output in the form of Newick and NEXUS format phylogenies), rates.csv (estimated diversification rates on the backbone phylogeny), and log.txt (extremely verbose output on what TACT is doing and why).

You should check the TACT results now for any issues:

$ tact_check_results Carangaria.tacted.newick.tre --backbone Carangaria.tre --taxonomy Carangaria.taxonomy.tre > checkresults.csv

Open up checkresults.csv in your favorite spreadsheet viewer and check the warnings column for any issues.