The Integrative Genome Viewer (IGV) supports multiple data formats. The Early Release Version of IGV (as of April 18 2011) supports viewing Goby alignments directly. You can download this version here.
In order to view goby alignments in IGV follow these simple steps:
- Select the menu item File->Load from File. This should present a dialog to select a file.
- Navigate to the directory that contains the alignments you wish to load in IGV.
- Choose a file that is part of a Goby alignment (any *.entries, *.header, *.tmh, *.index will work).
- Adjust the zoom level until the message ‘Zoom in to see alignment’ disappears.
- Navigate to a region of interest.
- Reads and sequence variations should be displayed in the track you created.
- Proceed to load other alignment or data tracks.
Here is a preview of three Goby alignment files loaded as separate tracks in IGV: