CHANGES IN VERSION 1.0.2 ------------------------- o Use 'multiFixationSites' for both single and multiple fixation sites CHANGES IN VERSION 1.0.1 ------------------------- o Bug fix: Error when adding new result in 'fixationSites' CHANGES IN VERSION 0.99.28 ------------------------- o Bug fix: Internal indexing error in 'multiFixationSites' o The default for 'makePlot' in 'sneakPeak' changed to False o The default 'tolerance' in 'fixationSite' changed to 0.01 o Improve visualization of 'fixationSites' return CHANGES IN VERSION 0.99.27 ------------------------- o Improve 'multiFixationSite' with a two-way greedy algorithm o Use dash line for excluded 'lineagePath' in 'plotSingleSite' CHANGES IN VERSION 0.99.26 ------------------------- o Bug fix: 'nodeAAsum' subscript out of bound in 'multiFixationSite' CHANGES IN VERSION 0.99.25 ------------------------- o Use amino acid color for 'plotSingleSite.fixationSite' o Add 'excluded' legend to 'plotSingleSite' o Update DESCRIPTION and NEWS o Use BiocStyle for vignettes CHANGES IN VERSION 0.99.6 ------------------------- o New functionality 'multiFixationSites' o Rewrite pruner functions o Add 'minPath' argument for 'sneakPeek' o 'sitePath' function's name changed to 'lineagePath' o Minimum entropy o The underlying data structure CHANGES IN VERSION 0.99.5 ------------------------- o Add new functionality 'addMSA' o Avoid 'root.phylo' function