Highlights of selected applications
- TraceView - DNA
chromatogram viewer
- GDE - Genetic Data Environment.
GDE
is a multiple sequence editor that reads sequences in a wide variety of
formats. Most BIRCH programs can be run using GDE, thereby unifying all
tasks in a single environment.
- SEQUIN - Submit sequence
data
to GenBank
- Cn3D
- Protein 3D structure viewer
- ARTEMIS
- Sequence feature visualization
- ClustalX - Multiple Sequence
Alignment
- Mesquite
- evolutionary and phylogenetic analysis workbench
- ospX - Oligonucleotide Search
Program
- ACeDB - Laboratory Database
- Taverna
- data pipeline design, using web services
On the CDE window system, most BIRCH programs can be launched from the
Molecular Biology submenu
of the Workspace menu. Simply hold down the right mouse button on the
workspace (background) area of the screen and drag right on "Molecular
Biology":
The one problem with launching molecular biology applications form
this menu, rather than the command line, is that when launched from the
menu, the default working directory is your home directory. Since most
molecular biology tasks are complex enough to merit specific
subdirectories for each project, this can result in a lot of "clicking
through directories". In contrast, when you launch an application from
the command line, the working directory is the directory you were in at
that time. In particular, GDE creates numerous temporary files and
directories. If launched from the Molecular Biology menu, GDE may
forget
to delete some of these files or directories, or may not be able to
find
files it needs. Therefore, GDE has been deliberately omitted from the
Molecular Biology menu.
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