Introduction

Introduction

EquiRep is a tool for finding tandem repeats in sequences. The data and scripts for reproducing the results of the paper are available here.

Dependency

EquiRep requires C++11 or later to compile and run successfully. Make sure your compiler supports C++11 by checking its version.

Installation

EquiRep can be easily installed via conda.

If you wish to install it from source code, download the source code of latest EquiRep from here.

Use the following commands to build EquiRep:

cd EquiRep
./configure
make

The executable file EquiRep will appear at src/EquiRep.

Usage

EquiRep processes an input FASTA file and generates an output FASTA file with the repeat units.

The usage of EquiRep is:

EquiRep <input_file> <output_file_prefix>

Arguments:

<input_file> - Path to the input FASTA file.

<output_file_prefix> - Prefix for the output FASTA file.

Running EquiRep on a small example

A small example of input data input.fasta is available in the example directory.

Commands to enter example directory and run EquiRep using input.fasta as input:

cd ./example
../src/EquiRep input.fasta output

An output file named output.fasta will appear in the example directory.