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bms_runner: Prediction of functional linkage from correlated gain and loss of genes
simpops.mac: Simulating population time series
LVB: Reconstructing Evolution with Parsimony and Simulated Annealing
PatQuest: Genetic marker based inference of paternity and impacts of
paternal traits on reproductive success

Supplementary information (as pdf) for the following paper:
Barker, D. 2004. LVB: Parsimony and simulated annealing in the search for phylogenetic trees. Bioinformatics, 20, 274-275
Revised supplementary text (as pdf) for the following paper:
Latysheva, N., Junker, V.L., Palmer, W.J., Codd, G.A. and Barker, D. 2012. The evolution of nitrogen fixation in cyanobacteria. Bioinformatics, 28, 603-606.