Merge pull request #39 from DannyArends/master

Help file by DA
minor

corecting formating of the print.population
bugfix

removing a lot of small bugs
bugfix

getting rid of Danny's shaba
bugfix

cross.denovo
gff files

preparing for handlign gff files
gff files

handling of these
gff file

handling
gff file

handling
renaming file

to comply with the function name
updates

new version, restoring correct maintainer
check.population

making it adhere to standards
minor bugfix
bugfix

few minor bugs
bugfix in transform function

n/x/matrix mixed up
adding gff handling
docs update
removing trash from test file
bugfix
bugfix + removing unnecessary code