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Additional files for 'Comparison of the protein-coding genomes of three deep-sea, sulfur-oxidising bacteria: "Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena' Genome-wide protein sets input to OrthoMCL, OrthoMCL output, Perl script to count cross-species occurence of OrthoMCL groups, and output of Perl script, as used by McGill and Barker (2017, BMC Research Notes, submitted).
simpops.mac: population time series simulation script from "The effects of environmental perturbation and measurement error on estimates of the shape parameter in the theta-logistic model of population regulation" The simpops.mac script simulates population time series for investigation of the effects of underlying parameters, environmental perturbation, measurement error and time series length on the estimation of theta in the ...
Preprocessed gene trees from 49 taxa of Cyanobacteria and 16 Proteobacteria used by Darby et al. (2017, Bioinformatics 33:640-649; doi:10.1093/bioinformatics/btw686) are provided here. These consist of trees for 13623 of ...
Phylogenetic trees for the orthologous groups predicted across 49 taxa of Cyanobacteria and 16 Proteobacteria by Latysheva et al. (2012, Bioinformatics 28:603-606; doi:10.1093/bioinformatics/bts008) are provided here. For ...