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Genomes and genes
Sequence tools 

retrieve sequence
retrieve EnsEMBL seq
fetch-sequences from UCSC
sequences from bed/gff/vcf
purge sequence
convert sequence
random sequences

Matrix tools 

Build control sets
Motif discovery
over-represented k-mers
oligo-analysis (words)
oligo-diff (words)
dyad-analysis (spaced pairs)
k-mers with positional biais
position-analysis (words)
local-word-analysis (word and spaced pairs)
k-mer assembly
pattern assembly
matrices
info-gibbs
Pattern matching 

Comparative genomics

NGS - ChIP-seq
Genetic variations 

Conversion/Utilities
Set comparisons / enrichment
Stats
Frequency distribution
sequences
convert sequence
matrices
convert matrix / logo
background models
create background
convert background
sequence probability
features
convert features
compare features
Drawing
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