There are six menu items: File, Algorithms, Options, Zoom In, Zoom Out, and Help.
File
There are two sub menu items: Open and Exit.
The input of the package can be done by three ways:
The Open menu item in the File menu allows users to select a source file to open. The default directory is the Data directory under the current working directory.
Input files can be prepared in any editor, but it is important that they are saved in Text Only ("flat ASCII") format. The format of the input file is the same as the PHYLIP package. Sequence alignment programs, such as ClustalW, commonly have an option to produce PHYLIP files as output, and some other phylogeny programs, such as MacClade and TreeView, are capable of producing a PHYLIP-format file. So, the output of these programs can also be used in this package.
The Exit quits the application.
Algorithms
The algorithms menu allows users to select four different algorithms: Fitch Margoliash, Maximum Parsimony, Neighbor Joining, and UPGMA. For the MP algorithm, only the DNA parsimony algorithm is implemented in the package.
Options
There are two menu items: Save Input and Pop Up Questions. By default, they are all enabled.
The Save Input option is helpful when the random data is produced. The data can be saved in a file, which is in the PHYLIP input file format. Then the file can be fed in the PHYLIP program to check the result.
The Save Input option is enabled when the program is first loaded. When users open a file from the File menu, the option is automatically disabled.
The Pop Up Question option is enabled when the program is first loaded. When the program is running in Run mode, the option is disabled. On the other hand, when the program is running in Trace mode, the option is enable by default. However, users can change the option anytime by checking or unchecking the option from the menu.
Zoom In
There are 10 sub menu items: 100%, 110%, 120%, 130%, 150%, 180%, 200%, 250%, and 300%. The default value is 100%.
This menu is very useful to let users enlarge the tree when the tree is too small. The default action is to enlarge the tree in the main phylogenetic tree area, not the trees in the Best Tree and the Previous State windows. One can use this option during the tree building and also with the final tree. The option works with the Zoom In menu to make the tree display in the small window as clearly as possible.
Zoom Out
There are 10 sub menu items: 100%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, and 10%. The default value is 100%.
This menu works in the same way as Zoom In menu.
Help
There are 4 sub menu items: PTC Help, Algorithms, Glossary, and About PTC.
PTC Help describes the PTC package. It consists of four parts:
The algorithms menu consists of four algorithms implemented in the PTC package. Each part describes the background information and the details of the algorithm.
Glossary contains the genetic terms used in the phylogenetic trees constructions. It is classified by the first letter of the term.
About PTC displays the version and contact information.
Send comments and suggestions about AHuffman to khuri@cs.sjsu.edu or cherryyang@yahoo.com