Perl scripts for working with the GFF format
Perl C
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BraceParser.pm
FileIndex.pm
GFFTransform.pm
README
SeqFileIndex.pm
SequenceMap.pm
blastexblx.pl
blasttransform.pl
cfilter.pl
cluster2gff.pl
exblx2dist.pl
exblx2gff.pl
exblxasym.pl
exblxcluster.pl
exblxextrapolate.pl
exblxfastcluster.pl
exblxgffintersect.pl
exblxindex.pl
exblxsingles.pl
exblxsort.pl
exblxsym.pl
exblxtidy.pl
exblxtransform.pl
genbank2gff.pl
gene.model
gff2exblx.pl
gff2ifetch.pl
gff2seq.pl
gffbytype.pl
gffdp.pl
gfffilter.pl
gffintersect.pl
gffmask.pl
gffmerge.pl
gffreverse.pl
gffrip.c
gffsects.pl
gffsort.pl
gffspan.pl
gffsubtract.pl
gfftransform.pl
hmm2gff.pl
hmmsearch2gff.pl
intersectlookup.pl
quickblastexblx.pl
spcwise2gff.pl
tandem2gff.pl
transposon.model

README

This repository contains Perl scripts for working with GFF
annotation files, including operations like sorting, merging and
intersection.

The scripts are hacky, unmaintained, and yet (presumably) largely
bug-free as they have been in production use at the Sanger Institute,
UC Berkeley and other locations since circa 1998.

For more information, please visit this URL:
http://biowiki.org/GffTools

If you use the tools, please cite my PhD thesis:
Holmes, I. PhD thesis. Dept of Genetics, University of Cambridge;
Wellcome Trust Sanger Institute. 1998.


Ian Holmes, UC Berkeley, August 2011