Argo Help
Overview
This is the main Argo help page. It provides links to the Argo help pages, which describe specific Argo features. The Argo help pages are also available from within Argo. For higher level documentation, see the User Guide and the FAQ; new users should consult these documents first.
If you haven't already, you can download argo here. No installation is required. If java 1.4 is properly set up on your system, you should be able to double click the jar file to start Argo. It may take a few seconds to start. For more detailed instructions, see the User Guide.
You may also run Argo as an applet or using java webstart.
Main Window Help
The Argo browser consists of three main windows:
Normally, Argo is used to inspect a single sequence at a time; however, you can also use the Argo Comparative View to inspect multiple, aligned sequences:
- Perpendicular View (default)
- Parallel View
Dialog Help
Dialogs are windows that let the user control the data and appearance of argo's three main windows. Some are very simple and only prompt for a single piece of information; these are described in the Menu help pages below. More complex dialogs are detailed here:
Menu Help
Almost all of Argo's functionality can be accessed through the menus. Each menu links to a help page:
Track Format Help
| Name | Viewable? | Exportable? | Editable? |
|---|---|---|---|
| BLAST | yes | no | no |
| Fasta | no* | yes | no |
| Genbank | yes | yes | no |
| Genscan | yes | no | no |
| GFF1 | yes | yes | yes |
| GFF2 | yes | yes | no |
| GTF2 | yes | yes | yes |
| GFF3 | yes | yes | yes |
| Wiggle | yes | no | no |
* Fasta files are viewable as sequences on which tracks may be imposed, not as tracks themselves.
Sequence Format Help
| Name | Can also contain tracks? |
|---|---|
| Fasta | no |
| Genbank | yes |
Alignment Format Help
| Name | Source |
|---|---|
| Simple Alignment | Broad |
| BLAST | NCBI |
| PatternHunter | Bioinformatics Solutions, Inc. |