Here you can find a full list of software developed by the group, with download links. If you have any questions about our software, need help running it, or you are interested in helping us improve it, then please get in touch!
Consensify generates pseudohaploid sequences from palaeogenomic data with reduced error rates compared with single read sampling, while controlling for biases resulting from differential sequencing coverage. The reduction in error rate can improve the accuracy of a range of downstream analyses, including phylogenetic analysis, population clustering, admixture analysis, and estimates of genetic distances.
TAPAS is a program for Testing of Alignment Parameters for Ancient Samples. TAPAS takes a reference genome and generate simulated palaeogenomic data from it. Critically, TAPAS retains the genomic location of the simulated ancient fragments which allows the precise quantification of mapping sensitivity and specificity when reads are mapped back to the original reference. In this way, the mapping algorithm and parameters can be fine tuned for specific animals and datasets.
The BEARCAVE offers a complete data repository, storage and processing environment. Handling large numbers of palaeogenomic datasets shared across multiple researchers poses several logistical challenges, including storage of data, sample and experiment information, and the automation and replication of basic data processing steps. Over several years we have developed solutions to these challenges, which we make publicly available as the BEARCAVE.
You can find out more about BEARCAVE and download it here
Phylogenetic test of geneflow direction
This is our method for determining the direction of gene flow in admixing lineages using low coverage palaeogenomic data. It was introduced in Barlow et al. 2018, where we used it to show that cave bears passed their alleles into recipient brown bear populations, where they still survive today. We are in the process of making the scripts publicly available, so please watch this space, or contact us for further details.