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
