ATV

From the ATV website, http://www.phylosoft.org/atv/:

ATV is a Java tool based on the FORESTER libraries for the visualization of annotated phylogenetic trees. It can be used both as an applet and as a standalone application. It requires Java version 1.5 or higher.

ATV reads three data formats:

New Hampshire — produced by all major phylogenetic analysis software

NHX — New Hampshire Extended — our extension of the NH format

phyloXML — an XML language which is currently in development

Installed on: codon.

Usage on codon

ATV can be used to display the tree file on a remote X-windows compatible computer. You MUST use a workstation or PC that can receive X-windows graphics. On such a machine, follow these steps:

On codon.psc.edu, instruct the computer where it is to send the remote graphics display by issuing this command:
```
setenv DISPLAY local-computer:0.0
```
where local-computer is your computer. This name will be of the form computer.site.type, such as ctc01.psc.edu. If you are unsure of the address of your system, type:
```
who -m
```
The name of your machine is given in parentheses at the end of the line.
Make sure that your local machines is set up to accept and display remote windows from codon.psc.edu.
Define CLASSPATH to be /biomed/src/SeqSpace/SeqSpace.jar. This is defined in the standard biomed login file, stored in /biomed/lib/examples/.login.fixed. You can:
```
setenv CLASSPATH /biomed/src/SeqSpace/SeqSpace.jar
```
to define CLASSPATH just for this session.

or, to set up all the definitions necessary for ATV and other biomedical programs, just for this session:
```
source /biomed/lib/examples/.login.fixed
```
or, to have all these definitions in effect each time at login:
```
cp /biomed/lib/examples/.login.fixed   ~/.login
```
Start the ATV program.
```
atv
```

ATV

Usage on codon

See also