Merge pull request #245 from ssjunnebo/574328_update_readme

574328 update readme

README.md

-# INTRODUCTION
+# The Artemis Software
+The Artemis Software is a set of software tools for genome browsing and annotation.
 
 [![Build Status](https://travis-ci.org/sanger-pathogens/Artemis.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Artemis)
+[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/Artemis/blob/master/LICENSE)
+[![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2F16.10.944-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/16.10.944)
 
-Artemis is a free genome browser and annotation tool that allows visualisation 
-of sequence features, next generation data and the results of analyses within 
-the context of the sequence, and also its six-frame translation.  Artemis is written 
-in Java, and is available for UNIX, Macintosh and Windows systems. It can read 
-EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. 
-Other sequence features can be in EMBL, GENBANK or GFF format.
+## Contents
+  * [Introduction](#introduction)
+  * [Installation](#installation)
+  * [Usage](#usage)
+  * [License](#license)
+  * [Documentation](#documentation)
 
-ACT is a free tool for displaying pairwise comparisons between two or more DNA 
-sequences. It can be used to identify and analyse regions of similarity and 
-difference between genomes and to explore conservation of synteny, in the context 
-of the entire sequences and their annotation.
+## Introduction
+The Artemis Software includes:
 
+* Artemis
+* ACT
+* BamView
+* DNAPlotter
 
-# DOCUMENTATION
+Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.
+
+ACT is a free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation.
+
+For further information, please see the [Artemis GitHub page](http://sanger-pathogens.github.io/Artemis/)
+
+## Installation
+
+For instructions on how to install Artemis, please see the [Artemis manual](ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf).
+
+## Usage
+
+For instructions please see the [Artemis manual](ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf)
+
+## License
+Artemis is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/artemis/blob/master/LICENSE).
+
+For more information on how to download Artemis, please see the [Artemis GitHub page](http://sanger-pathogens.github.io/Artemis/)
+
+## Documentation
 
 The Artemis user manual is at:
   http://www.sanger.ac.uk/science/tools/artemis
@@ -30,35 +54,3 @@ The BAM View user manual is at:
   http://www.sanger.ac.uk/science/tools/bamview
  
 
-# INSTALLATION
-
-The installation instructions are included in the user manual.
-
-
-# DISTRIBUTION
-
-Artemis may be freely distributed under the terms of the GNU Public License,
-and should run on any system with a recent version of Java.  
-
-For information on how to get Artemis see this web page:
-  http://www.sanger.ac.uk/science/tools/artemis
-
-
-# COPYRIGHT
-
-Copyright (C) 1998-2018  Genome Research Limited
-
-This program is free software; you can redistribute it and/or
-modify it under the terms of the GNU General Public License
-as published by the Free Software Foundation; either version 2
-of the License, or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-

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