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Graham Jones

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.

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).

DISSECT SOFTWARE

Dissect in BEAST. A jar file for using Dissect in BEAST1, a Dissect package for BEAST2, and a jar file for using SpeciesDelimitationAnalyser.

PUBLISHED ARTICLES

Calculations for multi-type age-dependent binary branching processes, Journal of Mathematical Biology, DOI: 10.1007/s00285-010-0362-8. Download PDF. The original publication is available at www.springerlink.com. Link.

Tree Models for Macro-Evolution and Phylogenetic Analysis. Systematic Biology 2011; doi: 10.1093/sysbio/syr086 Download pre-review version, Feb 2009.

Statistical Inference of Allopolyploid Species Networks in the Presence of Incomplete Lineage Sorting. Systematic Biology 2013; doi: 10.1093/sysbio/syt012. Download pre-review version, Aug 2012. It is also at arXiv.

PREPRINTS

On the reliability of Bayesian posterior clade probabilities in phylogenetic analysis (Jan 2008). Download PDF. It is also at Nature Precedings

DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent (Mar 2014). doi: 10.1101/003178. PDF at bioRχiv.

OTHER INFORMATION

My CV.

My other web site, with my artwork, is at at www.gjones.name.

Email: email address

See http://www.durness.org for information about the area I live in.