Author image Joachim Bargsten

Documentation

convert different alignment formats to another alignment format
convert mummer coords files to gff3 format
diff fasta files
find equal sequences
grep fasta files
convert mummer alignment files to clustalw format

Modules

Speedy functions to manipulate biological data
Utility functions for aligment stuff
IO class for the stockholm format
assembly related stuff
Identify Protein Domains with HMMER
a sequence feature
read and write gff files
make your blast result nice
remap ids of 'objects', should be used in IO-classes, like Bio::SeqIO
Library for simple matrix IO
Color phylogenetic trees in Dendroscope format
utility functions for phylogenetic analysis
analysis project utils
cluster sorted ranges iteratively
cluster overlapping ranges that are in the same group
find overlapping ranges
Gonzales Seqeuence Object
filter sequence data
fast utility functions for sequence IO
Utility functions for common tasks
convenience functions for yaml storage
functions handy for general development
Helper functions for all filesystem related tasks
functions handy for module development
Utility functions for file stuff
generate distinguishable colors in RGB format
Calculate kNN clusterings from already calculated distances
File input & ouput interface for parser classes
text and string functions
convenience functions for yaml storage

Provides

in lib/Bio/Gonzales/Align.pm
in lib/Bio/Gonzales/Align/ConsensePrimer.pm
in lib/Bio/Gonzales/Align/ConsensePrimer1.pm
in lib/Bio/Gonzales/Align/IO/MAF.pm
in lib/Bio/Gonzales/Align/Jalview.pm
in lib/Bio/Gonzales/Domain/Group.pm
in lib/Bio/Gonzales/Feat/IO.pm
in lib/Bio/Gonzales/Feat/IO/BED.pm
in lib/Bio/Gonzales/Feat/IO/Base.pm
in lib/Bio/Gonzales/Feat/IO/SWISS.pm
in lib/Bio/Gonzales/Graphics/Glyph/colorfulBox.pm
in lib/Bio/Gonzales/Matrix/IO/csv.pm
in lib/Bio/Gonzales/Matrix/Util.pm
in lib/Bio/Gonzales/MiniFeat.pm
in lib/Bio/Gonzales/Phylo/IO.pm
in lib/Bio/Gonzales/PrimarySeqIX.pm
in lib/Bio/Gonzales/Range/Util.pm
in lib/Bio/Gonzales/Role/BioPerl/Constructor.pm
in lib/Bio/Gonzales/Search/IO/HMMER3.pm
in lib/Bio/Gonzales/Seq/Filter/DuplicateSeqs.pm
in lib/Bio/Gonzales/Seq/IO/Fasta.pm
in lib/Bio/Gonzales/Seq/IO/fastq.pm
in lib/Bio/Gonzales/Seq/LongestTranscript.pm
in lib/Bio/Gonzales/Seq/Util.pm
in lib/Bio/Gonzales/Seq/Validate/fasta.pm
in lib/Bio/Gonzales/Tools/SeqMask.pm
in lib/Bio/Gonzales/Tools/SeqStats.pm
in lib/Bio/Gonzales/Domain/Identification/HMMER/SeqMarks.pm
in lib/Bio/Gonzales/Util/Log.pm
in lib/Bio/Gonzales/Matrix/IO/mcl.pm