Files

• Build.PL
• Changes
• LICENSE
• MANIFEST
• META.yml
• README
• 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/gitv_tex
• bin/gonz_compcol.pl
• bin/gonz_obo2dict.pl
• bin/gonz_overlap.pl
• bin/gonz_unmap.pl
• bin/gonzc
• bin/gonzconf
• bin/gonzlog
• bin/gonzp
• bin/headeridx.pl
• bin/instantblast.pl
• bin/iof.pl
• bin/merge_fa-qual.pl
• bin/newick2phyloxml.pl
• bin/ppt_profile_cmd.pl
• bin/ppt_profile_cmd_plot.R
• bin/ppt_watch_process.pl
• bin/self_dot_plot.pl
• bin/show-align2clustalw.pl
• bin/uniq_nodes.pl
• dist.ini
• 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/BED.pm
• lib/Bio/Gonzales/Feat/IO/Base.pm
• lib/Bio/Gonzales/Feat/IO/GFF3.pm
• lib/Bio/Gonzales/Feat/IO/SWISS.pm
• lib/Bio/Gonzales/GO/Util.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/MiniFeat.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/Project/Functions.pm
• lib/Bio/Gonzales/Project/Introduction.pod
• 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
• lib/Bio/Gonzales/Util.pm
• lib/Bio/Gonzales/Util/Cerial.pm
• lib/Bio/Gonzales/Util/Development.pm
• lib/Bio/Gonzales/Util/Development/File.pm
• lib/Bio/Gonzales/Util/Development/Module.pm
• lib/Bio/Gonzales/Util/File.pm
• lib/Bio/Gonzales/Util/Graphics/Color/Generator.pm
• lib/Bio/Gonzales/Util/IO/Compressed.pm
• lib/Bio/Gonzales/Util/Log.pm
• lib/Bio/Gonzales/Util/Math.pm
• lib/Bio/Gonzales/Util/Math/kNN/via/Distances.pm
• lib/Bio/Gonzales/Util/Role/FileIO.pm
• lib/Bio/Gonzales/Util/Text.pm
• t/00-load.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-IO-SWISS.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/Bio-Gonzales-Util-Cerial.t
• t/Bio-Gonzales-Util-File.t
• t/Bio-Gonzales-Util-Log.t
• t/Bio-Gonzales-Util-Log_threads.t
• t/Bio-Gonzales-Util-Math.t
• t/Bio-Gonzales-Util-Text.t
• t/Bio-Gonzales-Util.t
• t/IDMapIO.t
• t/Math-kNN-via-Distances.t
• t/Matrix-IO-mcl.distances
• t/Matrix-IO-mcl_phylip.distances
• t/accession.hmmresult
• t/boilerplate.t
• t/data/HMMSearch_Speruvianum.gff
• t/data/HMMSearch_Speruvianum.result
• t/data/example.pep.fa
• t/data/map.tsv
• 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/data/uniprot_sprot.dat
• t/data/uniprot_trembl.dat
• t/gonz_unmap.t
• t/idlist.txt
• t/manifest.t
• t/process_dummy.pl
• t/seqio-fasta-idmap.fa
• t/test.aln.phylip
• t/test.bed
• t/test.gff3
• t/test.hmm
• t/test.map