I am available to consult on bioinformatics / phylogenetics projects as well as for general IT and training packages; these services are provided through Kitson Consulting – contact them (email here) with project enquiries and they’ll be happy to provide a free consultation:
Kitson Consulting – Research support
Expert; Professional; Cost-effective: KCL is uniquely placed to add impact to your project, expand your team’s capabilities and facilitate your research, letting you concentrate on analysis and interpretation.
Phylogenetics
We offer extensive and in-depth expertise across a full set of cutting-edge phylogenetic analyses, from alignment, to reconstruction, to inferences of selection, recombination, migration, phylogeny-trait association, demography and signature epitope discovery. We use the latest proven methods and deliver high-quality, publication-ready outputs.
Services:
Sequence alignment, including reference/outgroup sequence selection, hypervariable region alignment optimization, sequence subtype/clade assignment and alignment summary statistics.
Phylogeny reconstruction (tree-building) using ML and state-of-the-art Bayesian MCMC methods, including full model selection.
Selection detection at single sites, sliding-windows or whole-sequence, over whole phylogenies or specific branches.
Recombination detection using GARD and bootscanning techniques.
Migration, demography (population dynamics) and phylogeographic inference based on Bayesian MCMC posterior sets-of-trees (bMCMC-PST) techniques that correctly incorporate phylogenetic uncertainty.
Ancestral sequence reconstruction via ML to assist in neutralization, infectivity and virulence assays.
Price structure: We are able to offer fast turnaround at unbeatable prices for alignment assembly, phylogeny reconstruction and selection/recombination detection. On receipt of your order we will quality-check the data package, confirm the type of analyses required and process your analysis on our dedicated phylogenetics servers.
For more complex projects and custom analyses, including custom algorithm design and implementation, we are more than happy to provide free initial consultations to determine the best approach for your data. Subsequent work will be billed at an agreed hourly rate with generous computer time included, up to an agreed maximum – so you can have confidence in project costs. We are happy to consider joint-authorship arrangements for involved projects.
Bioinformatics
Let us optimize storage, annotation, retrieval and management of your data, so you can extract maximum insight from it! We can advise on local, server-based and cloud-based solutions for conventional and high-throughput sequence data, GWA, neutralization and microarray data. We also have expertise in data-mining techniques, batch analysis and data pipeline optimization. Contact us now for a free consultation!
Statistics
We can help you select and carry out appropriate statistical analyses, as well as scaling your existing data analysis procedures up to large-scale studies using automated data pipelining. We can also advise on multiple test correction and Bayesian approaches.
Training
We firmly believe that good science rests on the dissemination of methodological expertise, as well as primary results. We can help your team build research capacity in the following areas:
- Principles of phylogenetics
- Basic phylogenetic analyses and best practice
- Phylogenetic inference
- Data mining
- Data warehousing for bioinformatics
- Data pipelines for bioinformatics
- Statistics for Life Sciences
