Changes in version 1.11.2 o More function availability for objects Changes in version 1.11.1 o Wrapper function for finding fixation and parallel sites o Core number set to 1 will disable multiprocessing Changes in version 1.9.4 o Fix: special case when tree root has more than one lineage path Changes in version 1.9.3 o Fix: invalid parallel mutations at divergent node. o Update DESCRIPTION, README and vignettes. Changes in version 1.9.2 o Allow partially plot 'lineagePath'. o Improved 'plotMutSites' function for 'lineagePath'. Changes in version 1.9.1 o Add 'useSites' argument to 'setSiteNumbering' function. o First 'stable' path as default 'lineagePath'. o Enable plot functions for 'parallelSites'. Changes in version 1.7.8 o Change default 'minSNP' value for 'parallelSites' function. Changes in version 1.7.7 o Fix: Add 'rmarkdown' in 'Suggests'. o Only plot paths with duplication in number for 'sneakPeek' function. Changes in version 1.7.6 o Bug fix: empty groups produced by 'groupTips' function. o Create 'paraFixSites' and 'fixationIndel' functions. Changes in version 1.7.5 o Treat 'phyMSAmatched' object as 'lineagePath' class for simplicity. o Improved multiprocessing. o Fix: repeated cluster name by '.assignClusterNames' internal function. o Rename 'allSitesPos' to 'allSitesName'. o Add 'plotMutSites' support for 'lineagePath' and 'fixationSites' objects. Changes in version 1.7.4 o 'cl.cores' option for turning multiprocessing on and off. Changes in version 1.7.3 o Fix: inability to get position of all the sites. Changes in version 1.7.2 o Fix: missing export for 'plot.phyMSAmatched' function. o Fix: 'addMSA' function unable to handle 'treedata' object. o Multiprocess for 'addMSA' and 'sitesMinEntropy' function. Changes in version 1.7.1 o Guess sequence type based on ATCG proportion for 'addMSA'. Changes in version 1.6.2 o Fix: Wrong ancestral node at divergent point (labeling issue). o Fix: Better strategy for conflicting 'AA' at divergent point. Changes in version 1.6.1 o Fix: Super slow 'lineagePath' computation improved and traded to 'addMSA'. o Fix: 'lumpyCluster' applies median to avoid outlier. o Bug fix: catch missing fixed mutation by going trough all paths. Changes in version 1.5.25 o Bug fix: use 'geom_point2' instead of 'geom_tippoint' to avoid error. Changes in version 1.5.24 o Add sequence type option for for DNA and amino acid. o Deprecate 'multiFixationSites' function. o Use 'y' argument as mutation label option in 'plot.sitePath' function. o Finer lineage resolving method used in 'lineagePath' function. Changes in version 1.5.23 o Create 'groupTips' functions to replace 'as.list' functions for 'fixationSites' and 'fixationPath' object. o Create 'sitesMinEntropy' function to output raw result of entropy minimization. o Create 'parallelSites' function and other functions for its return object such as 'plotSingleSite' and 'as.data.frame' Changes in version 1.5.22 o Fix missing newline when printing 'phyMSAmatched' object. o Create 'as.list.fixationSites' for retrieving grouped tips. o Remove 'tipname' option in 'as.data.frame.fixationSites'. Changes in version 1.5.21 o Fix wrong group name in some corner cases. o Use 'ggtree' for 'plotSingleSite'. Changes in version 1.5.20 o Further fix the merging issue in 'fixationSites'. Changes in version 1.5.19 o Speed up 'SNPsites'. Changes in version 1.5.18 o Bifurcation check for the phylogenetic tree and force bifurcation. o Fix path merging issue in 'fixationSites'. Changes in version 1.5.17 o Import 'aes' and 'theme' from 'ggplot2'. Changes in version 1.5.16 o Allow turning off mutation label for 'plot.fixationSites' while legend of cluster name becomes compulsory. o Import 'scale_color_manual' from 'ggplot2'. o Update vignette. Changes in version 1.5.15 o Bug fix: NA in cluster name. Changes in version 1.5.14 o Add 'as.treedata' function for 'fixationSites'. Changes in version 1.5.13 o Hierarchical naming of the clusters. Changes in version 1.5.12 o Establish 'phyMSAmatched' S3 class for better encapsulation. Changes in version 1.5.11 o Deprecate 'multiFixationSites' function. Changes in version 1.5.8 o Wrap mutations text in 'plot.fixationSites'. o Remove 'color' argument for 'plot.fixationSites' as the number of groups is usually unknown. Changes in version 1.5.7 o Left padding with 0 for the cluster name. o Add mutation label when plot 'fixationSites'. o Add 'as.data.frame' function for 'fixationSites'. Changes in version 1.5.6 o Add 'sitewiseClusters' function and plot function for its visualization. Changes in version 1.5.5 o Add 'plotMutSites' function to visualize mutations of each tree tip. Changes in version 1.5.4 o Use 'ggtree' for 'plot.lineagePath'. o More informative plot for 'sneakPeek' and add 'lineagePath' function for its return. Changes in version 1.5.3 o Add 'as.phylo.fixationSites' function that represent site fixations as simplified phylgenetic tree. Changes in version 1.5.2 o Add 'minEffectiveSize' in 'plot.fixationSites' for filtering small sized tip clusters. Changes in version 1.5.1 o Add 'plot.fixationSites' function. Changes in version 1.4.1 o Fix: broken link in the DESCRIPTION. Changes in version 1.3.1 o Bug fix: using sequence similarity failed to find 'lineagePath'. Changes in version 1.2.2 o Bug fix: infinity loop might occur when using 'fixationSites' or 'multiFixatoinSites' caused by internal function. There's no solution for version 1.2.x, so choices are given to possibly avoid it. o Bug fix: malfunctional 'setSiteNumbering'. Changes in version 1.2.1 o Bug fix: plot warning caused by 'tab' character o Bug fix: bad design causing 'multiFixationSites' extremely slow o Bug fix: 'fixationSites' gives replicated tips when combined Changes in version 1.1.10 o Allow user to choose whether to show tip labels in the plot functions Changes in version 1.1.9 o Add progress bar for the resampling and summarizing step of the function 'multiFixationSites' Changes in version 1.1.8 o Add 'plot' function for directly plotting the return of 'extractSite' o Apply resampling method for 'multiFixationSites' o The function 'fixationSites' applys the old 'multiFixationSites' Changes in version 1.1.7 o Add functionality 'extractSite' to allow accessing a single site from the result of 'fixationSites' and 'multiFixationSites' Changes in version 1.1.6 o Add functionality 'setSiteNumbering' to allow manipulating the reference of site numbering Changes in version 1.1.5 o Move similarity calculation to 'addMSA'. This will slow the function Changes in version 1.1.4 o Use total number of tips divided by number of nodes as 'minEffectiveSize' o Ignore invariant sites when search for fixation sites Changes in version 1.1.3 o Expose 'searchDepath' for 'multiFixationSites' Changes in version 1.1.2 o Use 'multiFixationSites' for both single and multiple fixation sites Changes in version 1.1.1 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