NearTree

What does it do?

NearTree will take a query SEQID, and then find the X closest strains to it out of a list specified by creating a phylogenetic tree and looking for the tips that are closest to your query strain.

How do I use it?

Subject

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

Description

The first line of the description should be the number of closest strains you want to your query strain. The second line must say query, and the third line should be the query SEQID you want to find close relatives for. The fourth line must say reference, and every line after that should be a SEQID you want to compare your query to.

Example

For an example NearTree, see issue 12940.

Interpreting Results

Upon completion, you'll be given a list of the SEQIDs that are closest to the query specified. The most closely related will be listed first, with each SEQID listed after that becoming slightly more distant.

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. NearTree 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.