EAGLE

An alignment-free tool to find relative absent words (RAWs) in genomic sequences

Introduction

What is EAGLE ?

EAGLE is an alignment-free method to find relative absent words (RAWs) in genomic sequences using a reference sequence. EAGLE has been published in Bioinformatics in May 2015.

It answers the following questions:

How do I get EAGLE ?

Clone our repository and run CMake command:
git clone https://github.com/pratas/eagle.git
cd eagle/src/
cmake .
make
Alternatively to CMake, run:
git clone https://github.com/pratas/eagle.git
cd eagle/src/
cp Makefile.linux Makefile
make

Usage

To see the possible options type
./EAGLE
or
./EAGLE -h
These will print the following options:
Usage: EAGLE <OPTIONS> ... -r [FILE]  [FILE]:<...>

  -v                       verbose mode,
  -a                       about EAGLE,
  -t                       use multi-threading,
  -i                       use inversions,
  -min <k-mer>             k-mer minimum size,
  -max <k-mer>             k-mer maximum size,

  -r  [rFile]              reference file (db),

  [tFile1]:<tFile2>:<...>  target file(s).

EAGLE is a fast method/tool to compute relative MAWs.
The input files should be FASTA (.fa) or SEQ [ACGTN].

License

GPL v3. For more information see LICENSE file or visit
http://www.gnu.org/licenses/gpl-3.0.html