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
