Merge pull request #1 from andrewjpage/master

Initial functionality
Merge pull request #2 from andrewjpage/master

working on real data
Merge pull request #3 from andrewjpage/master

vary memory usage according to input file size
Merge pull request #4 from andrewjpage/master

run mcl and inflate results
Merge pull request #5 from andrewjpage/master

typo in memory estimation
Merge pull request #6 from andrewjpage/master

speedup searching fastas
Merge pull request #7 from andrewjpage/master

transfer annotation
Merge pull request #8 from andrewjpage/master

extract proteomes from gffs and transfer anntotation as part of script
Merge pull request #9 from andrewjpage/master

label fasta sequences with annotation ID
Merge pull request #10 from andrewjpage/master

tests for create pan genome script
Merge pull request #11 from andrewjpage/master

catch undef
Merge pull request #12 from andrewjpage/master

check if group is null
Merge pull request #13 from andrewjpage/master

Find the difference between isolates
Merge pull request #14 from andrewjpage/master

Output statistics on groups
Merge pull request #15 from andrewjpage/master

create spreadsheets of differences between sets
Merge pull request #16 from andrewjpage/master

sort spreadsheet by number of isolates
Merge pull request #17 from andrewjpage/master

speedup extracting proteins from gff
Merge pull request #18 from andrewjpage/master

update tests for different input processing
Merge pull request #19 from andrewjpage/master

report more sequences from blastp
Merge pull request #20 from andrewjpage/master

inflate clusters where the representative gene is not the first