How to find Physcraper inputs

Physcraper takes as input a phylogenetic tree and the corresponding DNA alignment. This section shows how to get one for any given taxon from the OpenTree database using the Physcraper command line. If you already have a tree and an alignment of your own (or downloaded from somewhere else) that you want to update with Physcraper, please go to the Run section - Starting with your own tree.

Find a tree to update from OpenTree

The find_trees.py script searches for trees stored in OpenTree containing your taxon of interest.

Usage:

find_trees.py [-h] [-t TAXON_NAME] [-ott OTT_ID] [-tb] [-o OUTPUT]

Arguments:

-h , --help

Show the help message and exit.

-t TAXON_NAME, --taxon_name TAXON_NAME

A taxon name to search.

-ott OTT_ID, --ott_id OTT_ID

The OpenTree Taxonomy id number (OTT id) of the taxon to search.

-tb , --treebase

Return studies with TreeBASE data only.

-o OUTPUT, --output OUTPUT

File name (and path) of output file.

For example, to find all trees in OpenTree that contain one or more members of the Malvaceae, the family of flowring plants encompassing cotton, cacao, and durian, among others, you can do:

find_trees.py -t Malvaceae -o malvacea.txt

If you happen to know the taxon OTT id of the Malvaceae, or you have already obtained it from the OpenTree website taxon homepage, you can do:

find_trees.py -ott 279960 -o malvacea.txt

Find a corresponding alignment on TreeBASE

To find trees with a corresponding alignment on TreeBASE, use the flag -tb or --treebase:

find_trees.py -t Malvaceae -tb -o malvacea.txt