additional functions:
0.99.2
- modified 'lfm' method in order to accept different thresholds of p value or q value and conservation score
- removed the output folder:
 -> now all plots can be evaluated on the graphical device 
 -> clustalOmega output file is saved only if a path is provided either in 'alignSequences' method or 'setup' method
- in 'lmPlot' if the mode is 'gene' and only one sequence is analyzed, domains are represented within the plot and no logo plot and trident score are visualized
- the method 'paths' has been removed and all the options are now accessible through 'lmParams' method
0.99.3
- alignSequences can now run in web mode. No clustalo is necessary but the limit is set to 2000 sequences and a email address is required. In addition, perl must be installed in the system
- the newLowMACA constructor is now able to check all possible gene symbols, even if they are not protein coding genes or if they are not mapped in LowMACAAnnotation package
0.99.4
- custom perl command was added to the methods setup and alignsequences
bug fixes:
0.99.3
- add a conversion from U (selenocystein) to A in amino acid sequences while creating the LowMACA object ('newLowMACA' function) in order to fix a problem with .Trident_Score function
- modified check validity function in order to accept 'auto' in the bandwidth
- 'protter' method is now compatible with Windows OS
- a check was added in newLowMACA constructor to prevent more than one pfam ID entry by the user
0.99.4
- onLoad check added for:
	-> if "clustalo" is not in the PATH, a warning is raised
	-> if clustalo version is not 1.2.x, a warning is raised
	-> if XML:Simple and LWP modules for perl are not installed, a warning is raised
- check for exit status of clustalo system call added