# Change in 1.13.1

  o Add parameter output for getENCODEdata.

# Change in 1.9.6

  o Import pwalign.

# Change in 1.9.5

  o Update some Rd links to S4 links.

# Change in 1.9.4

  o Fix a warning in RMuscle cpp source.

# Change in 1.9.3

  o Fix some warnings in Muscle cpp source.

# Change in 1.9.2

  o Import subset method from S4Vectors.

# Change in 1.9.1

  o Fix the the potential issue for subset function by initial distance to NULL.

# Change in 1.7.1

  o Fix an issue for conflict constant INFINITY defineed in the system/math.h.

# Change in 1.5.3

  o Fix an stderr.

# Change in 1.5.2

  o try to fix the ambiguous `byte` reference by rename `byte` to `BYTE_8t`

# Change in 1.5.1

  o Remove stdout, stderr, cout, cerr, rand from source.

# Change in 1.3.4

  o Improve the speed for searchTFBP.

# Change in 1.3.3

  o Add reverseComplement for conservedMotifs search.

# Change in 1.3.2

  o Add support for multiple alignment for alignment function.
  o Add support for HTML output for the alignment.

# Change in 1.3.1

  o Add support for import GRanges directly for getENCODEdata.

# Change in 1.1.1

  o Fix the warning for enumeration value not handled in switch [-Wswitch]

# Change in 0.99.17

  o Try to get more error information from BioC build.

# Change in 0.99.16

  o Fix the wrong motif PWMs.

# Change in 0.99.15

  o Fix the wrong motif PWMs.

# Change in 0.99.14

  o Fix a typo in vignette.

# Change in 0.99.13

  o Add function searchTFBPS.

# Change in 0.99.12

  o Update the documentation.
  o Add motifConsensus argument for saveAlignments function.

# Change in 0.99.11

  o Fix typos in documentation.

# Change in 0.99.10

  o Add Makevars.win file to clean .o files in src.

# Change in 0.99.9

  o fix the make error: 'logf' was not declared in this scope.

# Change in 0.99.8

  o Change sprintf to snprintf for Muscle/typetostr.cpp:14:22.

# Change in 0.99.7

  o Remove functions contain fgets.

# Change in 0.99.6

  o Update the sample data al.

# Change in 0.99.5

  o Remove the so file from src folder.

# Change in 0.99.4

  o Remove the dependence of msa.

# Change in 0.99.2

  o Fix the issues listed in [#2181](https://github.com/Bioconductor/Contributions/issues/2181)

# Change in 0.99.1

  o fix the mis-link of genome in examples of alignment.

# Change in 0.99.0

  o Update the DESCRIPTION.
  o Update documentation of enhancers and saveAlignments

# Change in 0.1.2

  o drop ENCODExplorer.