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  About the Cambridge Cichlid Browser Site
A burtoni
Dominant male Astatotilapia burtoni
(Image: Russell D. Fernald and Sabrina S. Burmeister
published in the Public Library of Science)

Welcome to the Cambridge Cichlid Browser website. This site runs on the UCSC Genome Browser engine and contains the reference sequence and working draft assemblies for East African cichlid fishes and for other teleost genomes. It provides multiple alignment/conservation tracks and Lake Malawi variation data generated at the Sanger Institute (Malinsky et al., 2018; see "News" below), various genome-wide data tracks for a pair of cichlids from the crater lake Massoko (Malinsky et al., 2015) as well as various annotations generated by the Broad Institute (Brawand et al., 2014)

The Genome Browser zooms and scrolls over chromosomes, showing various annotations. Blat quickly maps your sequence to the genome. The Table Browser provides convenient access to the underlying database.

The Cichlid Genome Browser was developed and is maintained by Milan Malinsky, hosted at the Gurdon Institute, University of Cambridge. If you have feedback or questions concerning the tools or data on this website, feel free to contact Milan on mm21 at


6th December 2018 - Added the newAstatotilapia calliptera PacBio genome assembly

This high quality genome assembly provides the reference for some of our latest analyses. You will find the genome annotation and some experimental tracks under the fAstCal12 genome browser.

21st March 2017 - We are releasing a Variant Call File (VCF) for 73 Lake Malawi cichlid species

The VCF file contains genome-wide biallelic Single Nucleotide Polymorthism (SNP) variation for 134 individuals, covering 73 species and all the major lineages of the Lake Malawi haplochromine cichlid radiation. Further details with regards to the sample selection, methods and NCBI accessions for the raw genomic data are available in this PDF that accompanies the release.

The VCF file is now available for download: [VCF | index]. In addition, the new "malawiFilteredVCF" track has been added to the MetZeb1.1-prescreen Metriaclima zebra genome browser.

This is a public release in advance of publication of our genome-wide analysis of this dataset. It can be used without any restrictions for analyses concerning specific genomic region(s). If a genome-wide analysis forms a major part of a manuscript to be submitted before we publish on this dataset, we require the authors to contact us to discuss how to recognise our contribution in generating, preserving and sharing this resource.

17th January 2014 - 8 Species Cichlid/Teleost Conservation Track now available on MetZeb1.1-prescreen

After several months of CPU run-time and tens of thousands individual 'jobs' we are excited to announce the release of an 8 species alignment on the MetZeb1.1-prescreen Metriaclima zebra Genome Browser.

This new Conservation track shows multiple alignments of 8 species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package. For more information about the 8 species Conservation track, see its description page.

  Conditions of Use

The sequence and annotation data displayed in the Genome Browser are freely available for any use with a few restrictions that are noted within the species sections on the Credits page.