UGENE home page

Plugins

3D structure viewer

Visualization of biological 3D molecular structures.

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Available from version 1.3

3D structure viewer image

Workflow Designer

Allows to create and run complex computational workflows.

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Available from version 1.3

Workflow Designer image

Query Designer

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

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Available from version 1.9

Query Designer image

Chromatogram viewer

DNA chromatograms viewer/editor.

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Available from version 1.2


Chromatogram viewer image

Circular viewer

A circular viewer of a sequence.

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Available from version 1.6.2


Chromatogram viewer image

DNA Annotator

Search for sequence regions annotated with predefined set of annotations.

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Available from version 1.1

DNA annotator image

DNA export

Set of DNA sequence export and conversion utilities.

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Available from version 1.1

DNA export image

DNA graphs package

Draws graphs with various DNA sequence statistics.

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Available from version 1.0

DNA graphs package image

DNA statistics

Generates exportable statistical reports for sequences and alignments.

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Available from version 1.4

DNA statistics image

ORF marker

An utility to find open reading frames in DNA sequences.

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Available from version 1.2

ORF marker image

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

Remote query image

Repeat finder

Finds direct and invert repeats in DNA sequences.

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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.

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Available from version 1.5

Secondary structure prediction image

SITECON

Search for transcription factor binding sites in DNA sequence.

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Available from version 1.3

SITECON image

Smith-Waterman search

A complete Smith-Watertman search algorithm implementation

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Available from version 1.4

Smith-waterman search image

HMM2

Sequence analysis with profile hidden Markov models.

A graphical tools for using HMMs based on Sean Eddy’s HMMER 2 tool codebase.

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HMM2 image

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.

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Available from version 1.5

HMM3 image

uMUSCLE

A multiple alignment algorithm for protein and nucleotide sequences.

UGENE contains graphical port of Robert C. Edgar’s MUSCLE command line tool.

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Available from version 1.2

uMUSCLE image

Bowtie

A graphical port of the Bowtie short read aligner.

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Available from version 1.7

UGENE genome aligner

A fast short read aligner.

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Available from version 1.7

Weight matrix

Search for transcription factor binding sites in DNA sequence.

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Available from version 1.7

Weight matrix image

Dotplot

Builds dotplots for sequences and compare two biological sequences graphically.

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Available from version 1.7.1

Dotplot image

Primer3

Port of the Primer3 tool.

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Available from version 1.5

External tool support

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

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Available from version 1.7.2