This site is devoted to my interest in mathematical biology, especially phylogenetic analysis and macroevolution.
A bit about me. I completed a PhD in pure maths back in 1983. From the early 1990s to 2007 I mainly worked in the area of pattern recognition (more likely to be called machine learning or computer vision these days). I was self-employed, and wrote and marketed the optical music recognition program SharpEye. I worked at the Centre for Theoretical Biology in Gothenburg in 2011 and 2012. This was on phylogenetic methods for dealing with allopolyploids. I enjoyed this, but I do not want an academic career. I am not very rich, but I can afford to pursue my scientific interests without grants. I am in favour of open notebook science.
March 2020. If you are working on SARS-CoV-2 and think I might be able help with phylogenetic or phylodynamic analysis (especially BEAST2), maths, statistics, or scientific programming (R, Java, C++, CUDA) you are very welcome to contact me.
Working notes up to 2010.
Working notes 2011. Allopolyploids.
Working notes 2012. Allopolyploids.
Working notes 2013. Allopolyploids, species delimitation.
Working notes 2014. Species delimitation (DISSECT).
Working notes 2015. Species delimitation and tree estimation (STACEY).
Working notes 2016. STACEY. Various ideas.
Working notes 2017. DENIM. Isolation with migration.
Working notes 2018. DENIM. Isolation with migration.
Working notes 2019. Tinsmith chess engine.
Working notes 2020. Phylodynamic methods for SARS-CoV-2.
The Software page has information about the BEAST packages DISSECT, STACEY, and DENIM, and two command line tools. These are SpeciesDelimitationAnalyser which analyses the output from either DISSECT or STACEY, and Migration Analyser is a which analyses the output from DENIM.
If you have problems using these programs, please use the BEAST-users forum. I don't check the forum as often as emails, so feel free to send me an email as well.
This excludes some papers with many authors, where my contribution was a a small fraction of the whole, and some old papers. A fuller list is at my researchgate profile.
Graham Jones Divergence estimation in the presence of incomplete lineage sorting and migration. Advance article. Systematic Biology, syy041, https://doi.org/10.1093/sysbio/syy041.
Graham Jones Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of Mathematical Biology, 2016. DOI 10.1007/s00285-016-1034-0 Published version at Springer. Author version.
Jones G, Aydin Z, and Oxelman B. DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics 2014; doi = 10.1093/bioinformatics/btu770. Bioinformatics URL. Pre-review version, May 2014 at bioRχiv.
Bartoszek K., Jones G., Oxelman B., and Sagitov S. Time to a single hybridization event in a group of species with unknown ancestral history. J. Theor. Biol. 322 (2013) 1-6. arXiv preprint.
Jones G., Sagitov S. and Oxelman B. Statistical Inference of Allopolyploid Species Networks in the Presence of Incomplete Lineage Sorting. Systematic Biology 2013; doi: 10.1093/sysbio/syt012. Pre-review version, Aug 2012. It is also at arXiv.
Jones G. Tree Models for Macro-Evolution and Phylogenetic Analysis. Systematic Biology 2011; doi: 10.1093/sysbio/syr086 Pre-review version, Feb 2009.
Jones G. Calculations for multi-type age-dependent binary branching processes, Journal of Mathematical Biology, DOI: 10.1007/s00285-010-0362-8. PDF. The original publication is available at www.springerlink.com. Link.
On the reliability of Bayesian posterior clade probabilities in phylogenetic analysis (Jan 2008). Download PDF. It is also at Nature Precedings
My other web site, with my artwork, is at at www.gjones.name.
See http://www.durness.org for information about the area I live in.