CHANGES IN VERSION 1.6.5
-----------------------

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 1.6.3
-----------------------

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 1.6.2
-----------------------

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 1.6.1
-----------------------

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)
