Documentation
convert different alignment formats to another alignment format
grep fasta files
split sequences in fasta files by given regular expression
fasta file statistics
convert xlsx files to tsv format
convert mummer coords files to gff3 format
diff fasta files
find equal sequences
unmap or remap identifiers/strings using a given id mapping
matrix (CSV) data to xlsx format
track the cpu and memory usage of a command
convert mummer alignment files to clustalw format
organize your computational experiments
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 Sequence Object
filter sequence data
clean protein sequences
fast utility functions for sequence IO
represent experimental matrix-like data (assay) with features and sample info
Utility functions for common tasks
convenience functions for yaml and json IO
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
basic logging for Bio::Gonzales
Calculate kNN clusterings from already calculated distances
File input & ouput interface for parser classes
text and string functions
parse VCF files
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/CDhit.pm
in lib/Bio/Gonzales/Feat/IO/MUM.pm
in lib/Bio/Gonzales/Feat/IO/SWISS.pm
in lib/Bio/Gonzales/GO/Util.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/Project.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/Stat/Util.pm
in lib/Bio/Gonzales/String/Util.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/IO/Compressed.pm
in lib/Bio/Gonzales/Var/Util.pm
in lib/Bio/Gonzales/Matrix/IO/mcl.pm
Other files
Module Install Instructions
To install Bio::Gonzales, copy and paste the appropriate command in to your terminal.
cpanm Bio::Gonzalesperl -MCPAN -e shellinstall Bio::GonzalesFor more information on module installation, please visitthe detailed CPAN module installation guide.