### Version 1.3.3 ###
ADDITIONAL FUNCTIONS:
***
BUG FIXES:
- bug fix in .MakeUniformModel generic function because of sporadical crashes

### Version 1.3.2 ###
ADDITIONAL FUNCTIONS:
- Add CITATION
BUG FIXES:
- lfm method bug when using bw > 0
- little typo fix
- add on.exit par parameters fix 

### Version 1.1.51 ###
ADDITIONAL FUNCTIONS:
***
BUG FIXES:
- Simplified vignette and example in allPfamAnalysis and lfmSingleSequence

### Version 1.1.5 ###
ADDITIONAL FUNCTIONS:
***
BUG FIXES:
- Error handling for protter method. When Protter server is out of order, it returns an empty image with text

### Version 1.1.4 ###
ADDITIONAL FUNCTIONS:
***
BUG FIXES:
- Delete loading LowMACA objects for allPfamAnalysis in vignette

### Version 1.1.3 ###
ADDITIONAL FUNCTIONS:
***
BUG FIXES:
- Delete writing LowMACA objects for allPfamAnalysis in vignette and in the example

### Version 1.1.2 ###
ADDITIONAL FUNCTIONS:
***
BUG FIXES:
- new parallel implementation of allPfamAnalysis and lfmSingleSequence. nested parallel sections avoided and parallel back-end completely exposed to the user
- Parallelization in vignette and example reduced to 2 cores

### Version 1.1.0 ###
ADDITIONAL FUNCTIONS:
- New lfmSingleSequence method
- New lmPlotSingleSequence method
- New allPfamAnalysis function
- New checks for consistency of LowMACA object when methods entropy and mapMutations are called
- conservation is now a parameter of lmPlot, nullProfile and entropy methods too
- added the "datum" alignment option: when both a Pfam and genes are selected, LowMACA use the whole set of Pfam sequences to drive the alignment and then filters out only the selected sequences. In this way, every sequence in the Pfam mode will have the same position in the multiple alignemnt, disregarding the subset of sequences selected for the analysis.
- in Pfam mode, added the possibility to perform the alignment using HMM models downloaded from Pfam website (for example http://pfam.xfam.org/family/PF00001/hmm, for the HMM that is used to build the PF00001).
- lmPlot can split the consensuc sequence into smaller fragments to improve the readability of the plot
- the LowMACA vignette includes a section for "allPfamAnalysis" functionality 
BUG FIXES:
- Since "all" represents also the symbol of a kind of leukemia, the tumor type "all" was replaced by "all_tumors"
- Improvements to the vignette (inclusion of protter plot)
- Bug fix in lmPlot in reading boundaries of domains
- Typing error in parallelize method documentation fixed
- Some non-TCGA standard mutation types are now deleted from getMutations function ("Fusion" , "COMPLEX_INDEL" , "vIII deletion" , "Splice_Site_SNP" , "Indel")
- NAMESPACE was improved removing the import of the whole motifStack package and Biostrings package
- motifStack generic "plot" method was replaced with plotMotifLogo function to prevent conflicts with devtools load_all

### Version 1.2.1 ###
Add CITATION after BMC Bioinformatics publication