bin/agp2fasta.pl
bin/aln2aln.pl
bin/blast2gff3.pl
bin/consense_tree.pl
bin/coords2gff.pl
bin/fa2sto.pl
bin/fachar
bin/facompare
bin/fadiff
bin/faeq-seq
bin/faextract
bin/faextract_by_treeleaves
bin/faformat
bin/fagrep
bin/faln2phylip.pl
bin/fapair-identity
bin/farmgaps
bin/favalidate
bin/gff_to_bed.pl
bin/gffcds2seq.pl
bin/headeridx.pl
bin/instantblast.pl
bin/iof.pl
bin/merge_fa-qual.pl
bin/newick2phyloxml.pl
bin/project.pl
bin/self_dot_plot.pl
bin/show-align2clustalw.pl
Build.PL
Changes
lib/Bargsten/Bio.pm
lib/Bargsten/Bio/Align/Jalview.pm
lib/Bargsten/Bio/Domain/Identification/HMMER.pm
lib/Bargsten/Bio/Domain/Identification/HMMER/SeqMarks.pm
lib/Bargsten/Bio/Domain/Identification/InterProScan.pm
lib/Bargsten/Bio/IDMapIO.pm
lib/Bargsten/Bio/Matrix/IO/mcl.pm
lib/Bargsten/Bio/Phylo/Dendroscope.pm
lib/Bargsten/Bio/PrimarySeqIX.pm
lib/Bargsten/Bio/Role/BioPerl/Constructor.pm
lib/Bargsten/Bio/SearchIO/HMMResult.pm
lib/Bargsten/Bio/Seq/Filter/DuplicateSeqs.pm
lib/Bargsten/Bio/Seq/Validate/fasta.pm
lib/Bargsten/Bio/SeqIO/fasta/idmap.pm
lib/Bargsten/Bio/Tools/SeqMask.pm
lib/Bargsten/Bio/Tools/SeqStats.pm
lib/Bio/Gonzales.pm
lib/Bio/Gonzales/Align.pm
lib/Bio/Gonzales/Align/ConsensePrimer.pm
lib/Bio/Gonzales/Align/ConsensePrimer1.pm
lib/Bio/Gonzales/Align/IO.pm
lib/Bio/Gonzales/Align/IO/MAF.pm
lib/Bio/Gonzales/Align/IO/Stockholm.pm
lib/Bio/Gonzales/Align/Jalview.pm
lib/Bio/Gonzales/Assembly/IO.pm
lib/Bio/Gonzales/Domain/Group.pm
lib/Bio/Gonzales/Domain/Identification/HMMER.pm
lib/Bio/Gonzales/Domain/Identification/HMMER/SeqMarks.pm
lib/Bio/Gonzales/Feat.pm
lib/Bio/Gonzales/Feat/IO.pm
lib/Bio/Gonzales/Feat/IO/Base.pm
lib/Bio/Gonzales/Feat/IO/BED.pm
lib/Bio/Gonzales/Feat/IO/GFF3.pm
lib/Bio/Gonzales/Graphics/BLAST.pm
lib/Bio/Gonzales/Graphics/Glyph/colorfulBox.pm
lib/Bio/Gonzales/IDMapIO.pm
lib/Bio/Gonzales/Matrix/IO.pm
lib/Bio/Gonzales/Matrix/IO/csv.pm
lib/Bio/Gonzales/Matrix/IO/mcl.pm
lib/Bio/Gonzales/Matrix/Util.pm
lib/Bio/Gonzales/Phylo/Dendroscope.pm
lib/Bio/Gonzales/Phylo/IO.pm
lib/Bio/Gonzales/Phylo/Util.pm
lib/Bio/Gonzales/PrimarySeqIX.pm
lib/Bio/Gonzales/Project.pm
lib/Bio/Gonzales/Range/Cluster.pm
lib/Bio/Gonzales/Range/GroupedOverlap.pm
lib/Bio/Gonzales/Range/Overlap.pm
lib/Bio/Gonzales/Range/Util.pm
lib/Bio/Gonzales/Role/BioPerl/Constructor.pm
lib/Bio/Gonzales/Search/IO/BLAST.pm
lib/Bio/Gonzales/Search/IO/HMMER3.pm
lib/Bio/Gonzales/Seq.pm
lib/Bio/Gonzales/Seq/Filter.pm
lib/Bio/Gonzales/Seq/Filter/DuplicateSeqs.pm
lib/Bio/Gonzales/Seq/Filter/ProteinCleaner.pm
lib/Bio/Gonzales/Seq/IO.pm
lib/Bio/Gonzales/Seq/IO/Fasta.pm
lib/Bio/Gonzales/Seq/IO/fastq.pm
lib/Bio/Gonzales/Seq/LongestTranscript.pm
lib/Bio/Gonzales/Seq/Util.pm
lib/Bio/Gonzales/Seq/Validate/fasta.pm
lib/Bio/Gonzales/Tools/SeqMask.pm
lib/Bio/Gonzales/Tools/SeqStats.pm
MANIFEST			This list of files
MANIFEST.SKIP
README
t/00-load.t
t/accession.hmmresult
t/Align-Jalview.t
t/Bio-Gonzales-Align-IO.t
t/Bio-Gonzales-Align-Jalview.t
t/Bio-Gonzales-Domain-Group.t
t/Bio-Gonzales-Feat-IO-BED.t
t/Bio-Gonzales-Feat-IO-GFF3.t
t/Bio-Gonzales-Feat.t
t/Bio-Gonzales-Matrix-IO-mcl.t
t/Bio-Gonzales-Matrix-IO.t
t/Bio-Gonzales-Range-Cluster.t
t/Bio-Gonzales-Range-Overlap.t
t/Bio-Gonzales-Range-Util.t
t/Bio-Gonzales-Role-BioPerl-Constructor.t
t/Bio-Gonzales-Search-IO-HMMER3.t
t/Bio-Gonzales-Search-IO-HMMER3_no-hits.result
t/Bio-Gonzales-Seq-Filter-pep_clean.fa
t/Bio-Gonzales-Seq-Filter-pep_dirty.fa
t/Bio-Gonzales-Seq-Filter.t
t/Bio-Gonzales-Seq-IO-fastq.solexa.ref.cache.yml
t/Bio-Gonzales-Seq-IO-fastq.t
t/Bio-Gonzales-Seq-Util.t
t/Bio-Gonzales-Seq-Validate-fasta.t
t/Bio-Gonzales-Seq.t
t/Bio-Gonzales-Tools-SeqMask.t
t/boilerplate.t
t/data/example.pep.fa
t/data/HMMSearch_Speruvianum.gff
t/data/HMMSearch_Speruvianum.result
t/data/mini.fasta
t/data/rprot-domains_ebakker.fasta
t/data/starch_search_ioannis.hmmer3.reference_result.yml
t/data/starch_search_ioannis.hmmer3.result
t/data/test.aln.fa
t/data/test.aln.fa.no-relaxed.ref.phylip
t/data/test.aln.fa.relaxed.ref.phylip
t/data/test.aln.interleaved.phylip
t/data/test.aln.interleaved.ref.phylip
t/Domain-Identification-HMMER.t
t/idlist.txt
t/IDMapIO.t
t/idmapio.t
t/manifest.t
t/Matrix-IO-mcl.distances
t/Matrix-IO-mcl.t
t/Matrix-IO-mcl_phylip.distances
t/pod-coverage.t
t/pod.t
t/seq-validate-fasta.t
t/seqio-fasta-idmap.fa
t/seqio-fasta-idmap.t
t/test.aln.phylip
t/test.bed
t/test.gff3
t/test.hmm
t/test.map
t/tools-seqmask.t