Tools for Comparative Genomics


Import and Export files

Import (figure 1)

menu bar import
(Figure 1)

Display and query traits from a database:

Database connection file (.db) This type of files specifies all the elements required for TreeQ-VISTA to connect to a database, such information are database type, username, password, URL and driver class.
Tree description file (.tre) This type of files describes how a tree is stored in a database. The application assumes that the tree is flat. Each leaf of the tree, which takes up one row in a database, specifies the path from leaf to root and possibly the corresponding branch length if it is a phylogenetic tree.
Key description file (.ky) Ths type of file specifies where the keys are in a database. Each property (or annotation) is a pair of a key and a value. For example: COG.COG_ID = COG1035. Key is COG_ID which is a column name in the table COG, assignment is "=" and the value is COG1035. There are many other COG values in the table, though they are all listed in one column/Key COG_ID.
Query file (.qy) Thes types of files contains user pre-constructed queries that can be loaded into TreeQ-VISTA. Each entry of a file can be either a set of user constructed conditions from using TreeQ-VISTA or a SQL statement. History section records queries a user entered and history entries can be exported to a .qy file for future convenience.

Display traits from a Newick file:

Tree description file (.newick) This type of file is for describing a tree in a flat file. It has been a well accepted tree format. TreeQ-VISTA provides the functionality to display a phylogenetic tree and traits from a file, although the searching and querying capabilities are not provided for flat files. This is due to the immature query capabilities of flat files. Ex: there is no structured language similar to SQL that exists for flat file searching.
Group Description file (.grp) This type of files describes the name, color and which leaf nodes should be in a color group.

Export (figure 2)

(Figure 2)

Export Query History: Click on File->Export->Query History to export the available query history from the history section of the "More Queries" panel to a query file (.qy).
Export Tree Image (figure 3): (figure 5) Click on File->Export->Tree Image to see the dialog shown below. Choose the type of format and where you want to export and save the file to.

NOTE:  If you have an memory error, you can increase amount of memory available to Java virtual machine by changing the -Xmx###M parameter.

export Graphic image
(Figure 3)