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:

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

NameViewable?Exportable?Editable?
BLASTyesnono
Fastano*yesno
Genbankyesyesno
Genscanyesnono
GFF1yesyesyes
GFF2yesyesno
GTF2yesyesyes
GFF3yesyesyes
Wiggleyesnono

* Fasta files are viewable as sequences on which tracks may be imposed, not as tracks themselves.

Sequence Format Help

NameCan also contain tracks?
Fastano
Genbankyes

Alignment Format Help

NameSource
Simple AlignmentBroad
BLAST NCBI
PatternHunter Bioinformatics Solutions, Inc.

Last Updated: Sept 18 2006
Contact: Reinhard Engels
argo-support@broad.mit.edu