
In this directory are input files, 2 parameter files, and output files for 2 example
runs of MotEvo in its enhancer finding mode.

Input files:
input.fna = 4 regions from the Drosophila genome (10-15Kb in length) known to contain
an enhancer with sites for blastoderm WMs.
input.fna.ma = Multiple alignments of the same 4 regions with orthologs from other
Drosophila species.

wms_blastoderm = file with 7 weight matrices for TFs bicoid, caudal, dorsal, hunchback, knirps,
kruppel, and tailless.

motevoc_params = parameter file.
motevoc_params_ma = parameter file for the run with multiple alignments.


Example 1
------------
Here we run on the melanogaster sequence only. Since EMprior is set to 1 the priors are estimated in each window.
The priors are considered converged when they change by less than 5% (setting this lower will increase running
time). We use a window size of 450bps and a step length of 150 bps (about 1 nucleosome). Note that we use 
a second-order background model that is estimated directly from the input sequences.

command:
../../source/motevo input.fna motevoc_params wms_blastoderm > report

output files:
report = Report of MotEvo on parameters it read and running mode, etcetera.
crmfile = Enhancer scores and site densities for all windows.

Example 2
-------------
Here we run like in example 1, only now we just use 1 input region, and we now use multiple alignments of 
this region with orthologous regions from other Drosophila species. 

command:
../../source/motevo input.fna.ma motevoc_params_ma wms_blastoderm > report_ma

output files:
report_ma = Report of MotEvo on parameters it read and running mode, etcetera.
crmfile_ma = Enhancer scores and site densities for all windows.
