I was a post-doc with Mark from November 2011 to November 2013 but have now moved on to the lab of Sean Myles at Dalhousie University. My new contact information is:
Lab website: www.cultivatingdiversity.org
Personal website: www.danielmoney.co.uk/academia
E-mail: daniel.money <at> dal.ca
My research with Mark
I worked with Mark on methods for detecting and correcting a class of alignment errors: over compression. Each column in an alignment represents residues that should be inherited from a common ancestor. Under a strict interpretation of homology, each site in an alignment can be explained at most one insertion, but possibly multiple deletions. In a compressed alignment, residues inherited from an insertion event appear in the same column as residues that did not arise from that event. Our method compares site-likelihoods under a model that allows multiple insertions to site-likelihoods under a form of stochastic Dollo model which prohibits multiple insertions in the same column. Site-likelihood comparisons that favour multiple insertions can be used to guide the splitting of a single column into two or more columns in which all of the residues do appear to be homologous.
I'll leave links to my software here, in case anyone finds this site when looking for it.
- DupliphyML A tool for modelling gene family size evolution.
- GeLL A Java library for general likelihood calculations.