Allaby Research Group
Our various bioinformatics activities have led to the development of several tools which may be of use to other people or groups engaged in using large datasets. These are freely available to download from this page. Please give feedback if you want us to try and improve them.
Choose one of the items in the page below to go to its download page.
The TreeMos application provides a high-thoughput phylogenomic approach to search for and visualise phylogenetic mosaicism.
TreeMos is a high-throughput graphical analysis application that allows the user to search for phylogenetic mosaicism among one or more DNA or protein sequence multiple alignments and additional unaligned sequences.
TreeMos uses a sliding window and local alignment algorithm to identify the nearest neighbour of each sequence segment, and visualises instances of sequence segments whose nearest neighbour is anomalous to that identified using the global alignment. Data sets can include whole genome sequences allowing phylogenomic analyses in which mosaicism may be attributed to recombination between any two points in the genome. TreeMos can be run from the command line, or within a web browser allowing the relationships between taxa to be explored by drill-through.
This download is temporarily unavailable at this time.
FiPoDS takes two (possibly very large) FASTA files and searches one against the other sequence by sequence looking for local alignment hits that are top scoring but not identical. For each alignment, priming sites are identified to generate an (optionally nested) primer design for amplifying segments containing SNPs and indels. This is intended (and we use it) for trawling through genomic and/or mRNA data sets of pairwise taxa in order to find points of diagnostic divergence. We wrote this program to generate diagnostic PCR systems for closely related species that could not be distinguished by morphological traits.
MCMC_ODPR is used for designing degenerate primers. It uses Markov-Chain Monte Carlo to optimize primer reuse, thus by combining degenerate primers with reusable primers lowers the cost. MCMC_ODPR also allows primers to be designed within a range of melting temperatures and to be designed around SNPs. Constraints are in place to prevent primer-dimers and hairpin forming primers from being designed.