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README.md

1# The Artemis Software
2The Artemis Software is a set of software tools for genome browsing and annotation.
3
4[![Build Status](https://travis-ci.org/sanger-pathogens/Artemis.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Artemis)
5[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/Artemis/blob/master/LICENSE)
6[![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2F16.10.944-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/16.10.944)
7[![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtr703-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btr703)
8[![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtn529-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btn529)
9[![status](https://img.shields.io/badge/BIB-10.1093%2Fbib%2F4.2.124-brightgreen.svg)](https://doi.org/10.1093/bib/4.2.124)
10[![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbti553-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/bti553)
11[![status](https://img.shields.io/badge/BIB-10.1093%2Fbib%2Fbbr073-brightgreen.svg)](https://doi.org/10.1093/bib/bbr073)
12[![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtq010-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btq010)
13[![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtn578-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btn578)
14
15## Contents
16  * [Introduction](#introduction)
17  * [Installation](#installation)
18  * [Usage](#usage)
19  * [License](#license)
20  * [Documentation](#documentation)
21
22## Introduction
23The Artemis Software includes:
24
25* Artemis
26* ACT
27* BamView
28* DNAPlotter
29
30Artemis 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.
31
32ACT 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.
33
34For further information, please see the [Artemis GitHub page](http://sanger-pathogens.github.io/Artemis/)
35
36## Installation
37
38For instructions on how to install Artemis, please see the [Artemis manual](ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf).
39
40## Usage
41
42For instructions please see the [Artemis manual](ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf)
43
44## License
45Artemis is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/artemis/blob/master/LICENSE).
46
47For more information on how to download Artemis, please see the [Artemis GitHub page](http://sanger-pathogens.github.io/Artemis/)
48
49## Documentation
50
51The Artemis user manual is at:
52  http://www.sanger.ac.uk/science/tools/artemis
53
54The ACT user manual is at:
55  http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
56
57The DNA plotter user manual is at:
58  http://www.sanger.ac.uk/science/tools/dnaplotter
59
60The BAM View user manual is at:
61  http://www.sanger.ac.uk/science/tools/bamview
62
63
64