3D structure viewer

Available from version 1.3

Workflow Designer

Allows to create and run complex computational workflows.
(read more..)

Available from version 1.3

Query Designer

Allows to create and run complex query schemas which combine work of different algorithms via constraints.
(read more..)

Available from version 1.9

Chromatogram viewer

DNA chromatograms viewer/editor.
(read more...)

Available from version 1.2

Circular viewer

A circular viewer of a sequence.
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Available from version 1.6.2

DNA Annotator

Search for sequence regions annotated with predefined set of annotations.
(read more..)

Available from version 1.1

DNA export

Set of DNA sequence export and conversion utilities.
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Available from version 1.1

DNA graphs package

Draws graphs with various DNA sequence statistics.
(read more..)

Available from version 1.0

DNA statistics

Generates exportable statistical reports for sequences and alignments.
(read more..)

Available from version 1.4

ORF marker

An utility to find open reading frames in DNA sequences.
(read more..)

Available from version 1.2

Remote query

Annotates sequence by executing and scheduling requests to remote databases like NCBI-blast, CDD ...
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Available from version 1.2

Repeat finder

Finds direct and invert repeats in DNA sequences.
(read more..)

Available from version 1.4

Restriction enzymes

Marks restriction enzymes cut sites in DNA sequences
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Available from version 1.4

Secondary structure prediction

Protein secondarty structure prediction.
(read more..)

Available from version 1.5

SITECON

Search for transcription factor binding sites in DNA sequence.
(read more..)

Available from version 1.3

Smith-Waterman search

A complete Smith-Watertman search algorithm implementation
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Available from version 1.4

HMM2

Sequence analysis with profile hidden Markov models.
A graphical tools for using HMMs based on Sean Eddy's HMMER 2 tool codebase.
(read more..)

HMM3

The newest profile hidden Markov models tools.
Plugin contains an easy to use tools for HMMs build and search based on Sean Eddy's HMMER 3 tool.
(read more..)

Available from version 1.5

uMUSCLE

A multiple alignment algorithm for protein and nucleotide sequences.
UGENE contains graphical port of Robert C. Edgar's MUSCLE command line tool.
(read more..)

Available from version 1.2

Bowtie

A graphical port of the Bowtie short read aligner.
(read more..)

Available from version 1.7

UGENE genome aligner

A fast short read aligner.
(read more..)

Available from version 1.7

Weight matrix

Search for transcription factor binding sites in DNA sequence.
(read more..)

Available from version 1.7

Dotplot

Builds dotplots for sequences and compare two biological sequences graphically.
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Available from version 1.7.1

Primer3

Port of the Primer3 tool.
(read more..)

Available from version 1.5

External tool support

Allows to launch external tools (e.g. ClustalW, MAFFT) from UGENE.
(read more..)

Available from version 1.7.2