Basic usage instructions
Load an alignment in FASTA or CLUSTALW format using the File
-> Load alignment menu.
CAMA will automatically try to
detect the alphabet type. Make sure it gets it correct.
The windows is divided in 3 parts. The selection panel on the
left, the main plot in the middle and the alignment view at the
bottom.
Navigation
-
To move the plot, press the CTRL key and drag the plot the new
position. To zoom in and out of the plot, use the mouse wheel.
-
To switch through the differenct correspondance factors/axes,
use the two comboboxes at the top of the panel.
-
To rescale and center the plot back to see the big picture,
double click anywhere in the plot or hit the show all
button at the top of the panel.
-
To change the scaling of species and sites relative to one
another, use the right hand combo box in the panel above the
plot.
Selection
-
Drawing a rectangle with the mouse selects the contained
sequences (green circles) and sites (blue crosses). To add more
points to the selection, press the SHIFT key while selecting.
Clicking anywhere in the white area of the plot will erase the
current selection.
All selected sites and positions will be
automatically also selected in the alignment view (and vice
versa).
-
In order to save a selection, press CTRL and any number key from
1 to 0 simultaneously (e.g. CTRL+1). Pressing just the number
key will load the saved selection. Saved selections are
displayed in the lower left table and can be named by double
clicking the name.
-
In order to display labels for all currently selected sites,
press the S key, or use the View -> Show selected item
labelsmenu item.
Other features
-
Right clicking the logo panel between alignment view and plot
will turn the logo panel on and off. Left clicking switches
between sequence logo and conservation profile.
-
Right clicking the alignment view opens a window for changing
the colors of the alignment.