SaffronTree

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About
- Careers and Study
  Careers and Study
  Working at the Sanger Institute is truly unique. We put collaboration, innovation and support for people as individuals at the centre of everything we do. Join us to help shape the future by delivering life-changing science with the reach, scale, and creativity to solve some of humanity’s greatest challenges.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
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  - Careers
    Join our community of world class thinkers and professionals at the Sanger Institute located in Cambridge. Together we achieve life-changing science.
  - Study
    We are committed to training the next generation of pioneering genome scientists and clinicians. At the Wellome Sanger Institute we give PhD students and postdocs all the tools they need to succeed in the field of genomics research.
- Who we are
  Who we are
  Our vision and mission is to deliver world-leading genomics research in collaboration with research partners across the globe. Discover how our funding gives our leadership the independence to conduct bold, ambitious science that pioneers new fields in health, disease and conservation.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
  Read more
  - Our Vision
    By focusing on fundamental discovery research led by our faculty and employing our unique scale in cutting-edge data generation and analysis, we deliver discoveries not easily made elsewhere.
  - Impact
    From providing fundamental resources for understanding biology to exploring cancer genomes and the effects of variation in human genomes, our work lays the foundations for personalised medicine. We also reveal the secrets of human development and how infectious diseases evolve and spread.
  - Leadership and Governance
    Discover how our leadership and structures are designed to enable holistic and effective decision making, with transparency and accountability woven into their make up.
  - Strategy and Funding
    Read how our strategy informs our research focus and how our unique funding enables our scientists to take scientific risks to pioneer new approaches.
- Equality, Diversity and Inclusion
  Equality, Diversity and Inclusion
  The diversity in skills and knowledge that we all bring make our Institute the thriving ideas factory that it is. Discover how we support each other to reach our full potential and thrive. We celebrate diversity and seek to ensure that everyone has equal access to professional and career development opportunities.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
  Read more
- Policies
  Policies
  We play a pivotal role in helping to shape Government and International research policies. We also lead the way in developing guidance to support our scientists to carry out their research ethically, equitably and responsibly.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
  Read more
  - Influencing Policy
    We advise all levels of government both in the UK and across the world on the the role, impact and importance of genomic and life science research.
  - Research Policies
    Our policies help our researchers carry out their science collaboratively, equitably, ethically and responsibly.
- Admin Groups
  Admin Groups
  Browse our management and support operations teams that facilitate the Sanger Institute’s science.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
  Read more
- Campus Connections
  Campus Connections
  We are sited on the Wellcome Genome Campus at the very heart of a global hub of fundamental and applied genomic research, education and engagement. It is home to some of the world’s foremost institutes and organisations using genomes and biodata to deliver science with the reach, scale and imagination to solve some of humanity’s greatest challenges and maximise societal benefit.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
  Read more
About
We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
About Us
We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
Read more
Science
- Programmes
  Programmes
  Our research is organised into six primary Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus. In addition, our Associate Research programmes pioneer new approaches to studying health and disease.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
  Read more
- Groups
  Groups
  Browse the research, scientific and support teams in the Sanger Institute.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
  Read more
- Collaborations
  Collaborations
  Explore the national, international and global research projects and collaborations we either lead or actively contribute to.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
  Read more
- Data
  Data
  Browse our genomic and genetic data resources and repositories.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
  Read more
- Software and Resources
  Software and Resources
  We freely and openly provide the global research community with a wide range of genomics software, protocols, and platforms.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
  Read more
- Publications
  Publications
  The Sanger Institute has published papers in some of the most prestigious scientific journals. We aim to publish research that will transform biology and improve healthcare.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
  Read more
- Research Policies
  Research Policies
  Sanger Institute’s Research Policies are designed to provide guidance to help researchers navigate the legislation relating to their research and to ensure that research is ethical and legal.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
  Read more
- Archive
  Archive
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
  Read more
  - COVID-19
    The Sanger Institute played a major role in the genomic surveillance of the COVID-19 pandemic, providing large-scale high-throughput sequencing of the SARS-CoV-2 virus and analysis of its evolution and spread in the UK.
  - Sanger Seminar Series
    Throughout the COVID-19 lockdown of 2020-2021 we hosted a series of monthly freely available and open virtual seminars. From using genomic approaches to map all cell types in the human body, understand how cancer develops, and track the evolution and spread of global diseases, our senior scientists and faculty presented the latest developments in their field.
Science
Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease or analytic focus. In all cases, the studies provide insights into human, pathogen, cellular evolution, the phenotypic and hence biological consequences of genome variation and the processes which cause mutations.
Science & technology
Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
Read more
People
- Leadership
  Leadership
  Join us
  Our science is founded on the talents, imagination and curiosity of our people. Our wet-lab scientists, bioinformaticians, developers, engineers and skilled administrators work together to deliver cutting-edge research. Join us
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  - Sanger Leadership Team
    The Sanger Leadership Team is an Executive Committee that enables holistic and effective decision making, with transparency and accountability woven into its make up.
  - Governance
    How we are organised to enable transparent, open, responsive leadership.
  - Institute Scientific Advisory Board
    We draw on a number of experienced and internationally recognised scientists to provide independent scientific support, advice and challenge to help us maintain our scientific excellence.
- Faculty
  Faculty
  Join us
  Our science is founded on the talents, imagination and curiosity of our people. Our wet-lab scientists, bioinformaticians, developers, engineers and skilled administrators work together to deliver cutting-edge research. Join us
  Read more
  - Faculty
    Our Faculty conceive and deliver our science. Within our strategic framework the Institute’s scientific aspirations are driven by their vision, imagination and intellectual energy.
  - Associate Faculty
    Our Associate Faculty combine their skills and knowledge with the Sanger Institute’s unique abilities to conduct data generation and analysis at scale to pioneer genomic research in new areas.
  - International Fellows
    Our International Fellows Programme empowers early-career researchers with resources, mentorship, and funding to advance genomic research globally.
  - Honorary Faculty
    Our Honorary Faculty contribute to our research by providing insights and knowledge and collaborating on important research projects.
- All Sanger Staff
  All Sanger Staff
  Almost 1,000 scientists, developers, engineers and skilled professionals work together to deliver the Sanger Institute’s cutting-edge genomic research.
  Join us
  Our science is founded on the talents, imagination and curiosity of our people. Our wet-lab scientists, bioinformaticians, developers, engineers and skilled administrators work together to deliver cutting-edge research. Join us
  Read more
  - Science Staff
    From PhD students and Postdoctoral Fellows, bioinformaticians and laboratory managers, search for our staff who the support the delivery of pioneering science.
  - Non-Science Staff
    Look up our management and support staff that facilitate the Sanger Institute’s science.
People
Almost 1,000 scientists, developers, engineers and skilled professionals work together to deliver the Sanger Institute’s cutting-edge genomic research.
Join us
Our science is founded on the talents, imagination and curiosity of our people. Our wet-lab scientists, bioinformaticians, developers, engineers and skilled administrators work together to deliver cutting-edge research. Join us
Read more
Innovation
- Innovation at the Institute
  Innovation at the Institute
  We deliver therapeutic, diagnostic and production benefits in areas as diverse as cancer, immunology, public health and personalised treatment.
  Sanger Innovation
  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
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- For Industry
  For Industry
  Find out how our translation team maximises the socioeconomic impact of the Sanger Institute’s discoveries by translating our science into products, services and technologies that benefit patients in a variety of settings.
  Sanger Innovation
  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
  Read more
- For Researchers
  For Researchers
  Read how we benefit society by buiding on the innovative capabilities of our people by engaging with businesses and creating commercial opportunities. We also develop a unique and vibrant ecosystem to establish and grow innovative genomics and biodata businesses.
  Sanger Innovation
  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
  Read more
- Case Studies
  Case Studies
  Read examples of how we engage with funding, R&D, service and clinical communities to promote real-world utilisation of the Sanger Institute’s technologies and resources.
  Sanger Innovation
  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
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- Our Spin-Outs
  Our Spin-Outs
  We have a culture and history of scaling technologies. Some have become spin-out companies that positively impact today’s healthcare sector.
  Sanger Innovation
  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
  Read more
- Sanger Technologies
  Sanger Technologies
  Browse our technology and therapy opportunities.
  Sanger Innovation
  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
  Read more
Innovation
We deliver therapeutic, diagnostic and production benefits in areas as diverse as cancer, immunology, public health and personalised treatment.
Sanger Innovation
We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
Read more
News
- News and Blogs
  News and Blogs
  Read our latest news and stories of the science and people of the Sanger Institute.
  News and Blogs
  News and stories Announcements, articles and blogs from the cutting edge of genomic research.
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- Press Office
  Press Office
  The Communications team promote the Sanger Institute’s research and discoveries, using both traditional media such as print, radio interviews and TV footage and social media like Twitter, Facebook and the Sanger Institute blog
  News and Blogs
  News and stories Announcements, articles and blogs from the cutting edge of genomic research.
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- Branding and Logos
  Branding and Logos
  Wellcome Sanger Institute Branding Guidelines and Logos.
  News and Blogs
  News and stories Announcements, articles and blogs from the cutting edge of genomic research.
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Latest News

12 Nov 2024

Unlocking the genetics of skin cancer
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8 Nov 2024

A melody of bases: How scaling allows us to set new bars
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4 Nov 2024

Claire Chewapreecha wins the 2024 Nature inspiring women in science: Scientific Achievement prize
Read more

News and Blogs
News and stories Announcements, articles and blogs from the cutting edge of genomic research.
Read more

SaffronTree

A software application for fast, reference-free pseudo-phylogenomic trees from reads or contigs.

Quickly build a tree directly from raw reads or from assembled sequences, without the need for a reference sequence or de novo assemblies.

Downloads

Please see our GitHub page for download and installation instructions.

Further information

Learn and support

For more information and advice on using this software please see our GitHub page

License and Citation

SaffronTree is available under GPL3.

If you make use of this software in your research, please cite as:

“SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs”, Andrew J. Page, Martin Hunt, Torsten Seemann and Jacqueline A. Keane. The Journal of Open Source Software, 2(13), 2017. http://joss.theoj.org/papers/10.21105/joss.00243

Contact

If you need help or have any queries, please contact us using the details below.

If you need help or have any queries, please contact us using the details below.

Email: path-help@sanger.ac.uk

Our normal office hours are 8:30-17:00 (GMT) Monday to Friday.

Sanger Institute Contributors

Previous contributors

Photo of Dr Andrew Page

Dr Andrew Page

Principal Computer Programmer