Name Map

Name Map

The name map file allows the user to automatically map names it the Newick tree file to something more useful for display or publication.

Format

The name map is a two-column plain text file. The first column is the original name. This will be matched against the leaf labels in the tree. The second column is the new name. The new name may include spaces and symbols, even those that are not allowed in the Newick spec.

An example

Here is an example. Assume the tree looks like this

(s1,(s2,s3));

And the name map

#Old name	New Name
s1	E. coli (str. Sakai)
s2	S. flexneri

In this case, node s1 would appear as E. coil (str. Sakai), s2 would appear as S. flexneri, and s3 would remain unchanged.

Using a Name Map with a Color Map

Note that the color map will match against original names, not new names. This means that the for the above tree the following color map will work as expected

#Name	Color
s1	blue
s2	green
s3	orange

but this color map will only add color to s3.

#Name	Color
E. coli (str. Sakai)	blue
S. flexneri	green
s3	orange

See Iroki annotation precedence for more information about the order in which Iroki handles complex customization.