Tools for Comparative Genomics

 
 

Tree Description File (.tre)

Comments:

Line 1: specify the delimiter you would like to use to format the file such as --###--
Line 2: specify a text name of your tree. This is anything you wish to call your tree. It does not have to be the table name of the tree in database.
Line 3: specify in which table in the database the tree is stored.
Line 4 - Line x: specify the column names in the tree table constitute a path from root to leaf. When the tree is built, level 0 is the root, level 1 in the example below is DOMAIN, level 2 is PHYLUM and TAXON_NAME is the leaf level of the tree etc. Associated with each column names is column types and column types are required. You can enter branch length as well. See sample files.
Line x+1: The last line in the file specify by which column can a node be uniquely identified. This is usually the primary key of the tree table. This is used to eliminate duplicates resulting from complex queries where multiple records are returned but with same information.

Example:

delimiter--###--
name--###--IMG Taxon Tree
table--###--TAXON
level--###--DOMAIN--###--VARCHAR(255)
level--###--PHYLUM--###--VARCHAR(255)
level--###--IR_CLASS--###--VARCHAR(255)
level--###--IR_ORDER--###--VARCHAR(255)
level--###--FAMILY--###--VARCHAR(255)
level--###--GENUS--###--VARCHAR(100)
level--###--SPECIES--###--VARCHAR(100)
level--###--TAXON_NAME--###--VARCHAR(255)
unique--###--TAXON_OID

Also available:

SampleTaxonTreeDerby.tre
SampleTaxonTreeWithDistance.tre