more efficient find_gaps function using Rcpp
use Rcpp to map genomic positions
test
More efficient degapping and gapping of alignments
map genome2alignment, alignment2genome, genome2genome
re-roxygenise
new sliceAlignment()
Lots of fixes and speed improvements
fix NAMESPACE
aggregateAlignment function
Fix path to dependency intaller
update dependencies
fix NAMESPACE
Adapt to API change in biofiles
update install script for dependencies
change paths to install script
install muscle as dependency
Check for Genbank files ending with CONTIG instead of ORIGIN
remove dependency on rmisc; switch from Rentrez to reutils
orthology mapping