Blixem, which stands for BLast matches In an X-windows Embedded Multiple alignment, is an interactive browser of pairwise Blast matches that have been stacked up in a master-slave multiple alignment. It is thus not a 'true' multiple alignment, such as produced by e.g. Clustalw, but a 'one-to-many' alignment.

The command line usage for blixem is in the format blixem [options] {sequencefile} {datafile} [X options]

Both "sequencefile" and "datafile" can be substituted by "-" for reading from stdin (pipe). If "sequencefile" is piped, the first line should contain the sequence name and the second the sequence itself.

Options can be:
-s {mode} Sorting mode at startup.

• s = by Score
• i = by Identity
• n = by Name
• p = by Position

-I Inverted sorting order
-b Don't start with Big Picture
-S {#} Start display at position #.
-F {file} Read in query sequence and data from (replaces sequencefile).
-h Help and more options.

Some X options can be:
-acefont {font} Main font.
-font {font} Menu font.

To make the datafile from blast output, run MSPcrunch with option -q.

Related Resources from Sonhammer group see: here

References:
Sonnhammer, ELL and Durbin, R (1994). A workbench for Large Scale Sequence Homology Analysis. Comput. Applic. Biosci, 10:301-307. [ENTREZ]

Sonnhammer, ELL and Durbin, R (1994). An expert system for processing sequence homology data. ISMB 2:363-368 [ENTREZ]