formatted and added author attribution
moved blogo resource
moved blogo resource
moved older Arensburger project files to other folder
formatting and small changes
fix some typos for using the refs
Merge branch 'master' of github.com:stajichlab/mTEA into codereview_Jason

Conflicts:
	scripts/activeTE_msa.pl
make GFF use join instead of simplify tab delimited printing
added Sofia as author
minor fixes
removed realign step
added mismatch from consensus,removed all flag seqs from final aln
adj tir starts. correct 0/1 issue in intial tir finding
added consensus and gap filter subroutines
fixer scope errots
i forgot what we did
added print_fasta.fixed element_info print
added use Bio::SeqIO
fixed bio::seqIO new in sub print_fasta
fixed bio::seqIO new in sub print_fasta