CHANGES IN VERSION 1.13.8
-----------------------

NEW FEATURES

    o improve plot plotMotifStackWithPhylog.
      
CHANGES IN VERSION 1.13.7
-----------------------

    o update the documentation
    

CHANGES IN VERSION 1.13.6
-----------------------
BUG FIXES

    o fix bug when plot 2 motifs with motifStack function.


CHANGES IN VERSION 1.13.5
-----------------------

NEW FEATURES

    o improve the algorithm of DNAmotifAlignment. Replaced the ALLR by average 
      information content.

CHANGES IN VERSION 1.13.4
-----------------------

NEW FEATURES

    o improve the algorithm of DNAmotifAlignment

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.13.3
-----------------------

NEW FEATURES

    o add reorderUPGMAtree function

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)


CHANGES IN VERSION 1.13.2
-----------------------

NEW FEATURES

    o add mergeMotifs function

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)


CHANGES IN VERSION 1.13.1
-----------------------

NEW FEATURES

    o add plotMotifOverMotif function

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.11.8
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o Fix the bugs if background values don't have a name.

CHANGES IN VERSION 1.11.7
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o Fix the bugs in readPWM

CHANGES IN VERSION 1.11.6
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o Fix the bugs in motifCircos when input r.pfm and r.pfm2

CHANGES IN VERSION 1.11.5
-----------------------

NEW FEATURES

    o export $ and $<- methods for classes

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.11.4
-----------------------

NEW FEATURES

    o add function getRankedUniqueMotifs and pfm2pwm

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.11.3
-----------------------

NEW FEATURES

    o add function motifPiles

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.11.2
-----------------------

NEW FEATURES

    o export function highlightCol
    o add function motifCircos

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.11.1
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o Change the format of help file to avoid lines wider than 90 characters NOTE

CHANGES IN VERSION 1.9.9
-----------------------

NEW FEATURES

    o Add distance axis for plotMotifStackWithRadiaPhylog

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.9.8
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o fix the bug draw motif outside of canvas when plotMotifStackWithRadiaPhylog

CHANGES IN VERSION 1.9.7
-----------------------

NEW FEATURES

    o Change the position of motifs index when plotMotifStackWithRadialPhylog.

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)


CHANGES IN VERSION 1.9.6
-----------------------

NEW FEATURES

    o Increase the size of motifs when plotMotifStackWithRadialPhylog.

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.9.5
-----------------------

NEW FEATURES

    o Change default of plotIndex to FALSE when plotMotifStackWithRadialPhylog.

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.9.4
-----------------------

NEW FEATURES

    o Restyle index number when plotMotifStackWithRadialPhylog.

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.9.3
-----------------------

NEW FEATURES

    o Add index number when plotMotifStackWithRadialPhylog.

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.9.2
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o Fix bugs using motifDB in tests.

CHANGES IN VERSION 1.7.8
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o Fix bugs for motifSignature when the distance is larger than
    maximal distance.

CHANGES IN VERSION 1.7.7
-----------------------

NEW FEATURES

    o add ic.scale parameter to plotMotifLogo.

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.7.6
-----------------------

NEW FEATURES

    o Change the class of signature to include the color sets.

BUG FIXES

    o Allow motifSignature to accept Non-Binary Trees.

CHANGES IN VERSION 1.7.5
-----------------------

NEW FEATURES

    o Change the output of motifStack for further steps.

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.7.3
-----------------------

NEW FEATURES

    o Change the output of readPCM from a matrix to a list of 
    pcm objects.

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.7.2
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o fix the bugs of changing plot layout when using plotMotifLogoStackWithTree


CHANGES IN VERSION 1.7.1
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o fix the bugs of leave names and plot region

CHANGES IN VERSION 1.5.4
-----------------------

NEW FEATURES

    o use BiocStyle to write vignette

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.5.3
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o fix the bug that motifStack can not plot color correctly for 
    radialPhylog layout in motifStack(). 

CHANGES IN VERSION 1.5.2
-----------------------

NEW FEATURES

    o use log-likelihood ratio (ALLR) to do alignment

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)


CHANGES IN VERSION 1.5.1
-----------------------

NEW FEATURES

    o plotMotifStackWithRadialPhylog can draw motif cloud in 
      RadialPhylog style. Check vignette to see the details

BUG FIXES

    o check mode of pcm and pfm matrix, which should be numeric



CHANGES IN VERSION 1.2.12
-----------------------

NEW FEATURES

    o New methods add to pcm and pfm class.

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.2.10
-----------------------

NEW FEATURES

    o New function motifStack
    o motifCloud function is separated into two functions: motifSignature
    and motifCloud
    o New class pcm and motifSig

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)


CHANGES IN VERSION 1.2.9
-----------------------

NEW FEATURES

    o New layout for function motifCloud to draw motif cloud

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)


CHANGES IN VERSION 1.2.8
-----------------------

NEW FEATURES

    o New function motifCloud to draw motif cloud

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)


CHANGES IN VERSION 1.2.7
-----------------------

NEW FEATURES

    o Shorten the execution time

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.2.6
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o Fix bug object 'rayonWidth' not found when the pfms is not given
    for plotMotifStackWithRadialPhylog()

CHANGES IN VERSION 1.2.5
-----------------------

NEW FEATURES

    o Append a set of color prameter to control
    the behavior of plotMotifStackWithRadialPhylog()

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.2.4
-----------------------

NEW FEATURES

    o Append a prameter clockwise, init.angle and angle to control
    the behavior of plotMotifStackWithRadialPhylog()

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)

CHANGES IN VERSION 1.2.3
-----------------------

NEW FEATURES

    o No changes classified as 'new features' (package under active
    development)

BUG FIXES

    o fix the bug that plots x-axis repeatedly in plotMotifLogo(). 


CHANGES IN VERSION 1.2.2
-----------------------

NEW FEATURES

    o Append a prameter revcomp indicates whether the DNAmotifAlignment
    should use reverse-complement motif for alignment.

BUG FIXES

    o Append a prameter rcpostfix, defaut is "(RC)", to the name slot
    of the pfm when DNAmotifAlignment using reverse-complement motif
    for alignment.

CHANGES IN VERSION 1.2.0
-----------------------

NEW FEATURES

    o draw aligned motif logo stacks with phylogenetic tree in radial style

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)


CHANGES IN VERSION 1.0.0
-----------------------

NEW FEATURES

    o draw DNA/RNA sequence logo

    o draw Amino Acid sequence logo

    o draw aligned motif logo stacks with phylogenetic tree

BUG FIXES

    o No changes classified as 'bug fixes' (package under active
    development)
