shadow [options] <tree> <alignment>


Perform phylogenetic shadowing on a given DNA alignment, using a given tree (Boffelli et al, Science 2003). This program is a simplified version of motiph, in which the equilibrium distribution is set equal to the background model, rather than being taken from a given motif.

Input: Output:

Shadow will create a directory, named shadow_out by default. Any existing output files in the directory will be overwritten. The directory will contain:

The default can be overridden using the --o or --oc options which are described below.

The --text will limit output to plain text sent to the standard output.
Options: Warning messages: None