DiversiTree

What does it do?

DiversiTree is used for creating phylogenetic trees using parsnp, and optionally finding a specified number of strains that represent the most genetic diversity.

How do I use it?

Subject

In the Subject field, put DiversiTree. Spelling counts, but case sensitivity doesn't.

Description

The first line of the description should be the number of diverse strains you want picked. If all you want here is the tree and don't care about the number of strains, you can set this to 1. Subsequent lines should be the SEQIDs you want to create the tree from. Note that these strains should all be fairly closely related, or the tree creation may fail (so try to keep things to the same species).

By default, DiversiTree uses a tree creation program called parsnp. Another option available is mashtree, which is generally faster at making trees and can handle more diversity between samples, but may create less accurate trees. If you want to use mashtree, add a line at the end of your description that says treeprogram=mashtree. You can look at issue 14724 for an example request that uses mashtree.

Example

For an example DiversiTree, see issue 12100.

Interpreting Results

DiversiTree will upload two files to Redmine on completion: diversitree_report.html, and tree.nwk. The diversitree.html can be opened in any web browser, and has a picture of the tree with selected strains highlighted, and a list of the X most diverse strains, where X is the number specified in the first line of the description. The tree.nwk file contains the phylogenetic tree created in newick format. If you want to view this tree, you can use a program such as FigTree or a web-based viewer like phylo.io.

How long does it take?

This depends largely on the number of strains you want to use to create the tree. It can often be as quick as a few minutes if you have 10 or less strains, or take several hours if you want a larger (100 or so strain) tree.

What can go wrong?

A few things can go wrong with this process:

1) Requested SEQIDs are not available. If we can't find some of the SEQIDs that you request, you will get a warning message informing you of it.

2) Strains too far apart. DiversiTree will warn you if it thinks that the strains you want to make a tree from are not closely related enough. If you get this warning, you may want to consider creating a new issue while leaving out the strains it says are too far, or use mashtree as your tree creation program.