---
name: "ugene"
section: "1"
platform: "linux"
package: "ugene"
version: "51.0+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ugene"
---

# ugene(1)

integrated bioinformatics suite

## NAME

**UGENE** - integrated bioinformatics suite

## SYNOPSIS

**ugene** -ui

**ugene** \[*OPTIONS*\]

## DESCRIPTION

**UGENE** is a cross-platform environment for DNA and protein sequence analysis. **UGENE** integrates the most popular bioinformatics computational algorithms and provides both GUI and command line interface for performing complex analysis of the genomic data.

The main features of **UGENE**:

- \*

  View and analysis of annotated DNA or protein sequences

- \*

  Chromatograms visualization and editing

- \*

  Integrated 3D viewer for files in PDB and MMDB formats

- \*

  Integrated support of search requests to NCBI databases

- \*

  Multiple sequence alignment using MUSCLE3, MUSCLE4 and KAlign

- \*

  HMM profiles build and search, based on the source of HMMER2 and HMMER3

- \*

  Modern protein secondary structure prediction algorithms based on GORIV and PsiPred

- \*

  Phylogenetic analysis with Phylip

- \*

  PCR Primers design using Primer3 package

- \*

  Cloning in silico

- \*

  Search for transcription factor binding sites in DNA sequences using SITECON

- \*

  Search for restriction enzymes and integration with REBASE

- \*

  Search for direct and invert repeats

- \*

  DNA reference assembly using Bowtie

- \*

  Protein back translation

- \*

  Search for ORFs

- \*

  Designer for complex computational workflows and queries

**UGENE** has modular structure and almost all its functionality comes within plugins. Internally **UGENE** is designed with support of parallelism to make profit from using multicore computers. Every computational task in **UGENE** is performed in background and does not block user interaction with graphical interface.

## OPTIONS

- **-ui**

  run GUI version of **UGENE**

- **--help**

  print a usage message briefly summarizing all command-line options and the program version, then exit.

- **--license**

  dump license information

- **--task=\<path-to-schema or schema-name\> \[schema-options\]**

  run given workflow schema

- **--status-bar-hide**

  don't show task status bar

- **--ini-file=\<path-to-settings-file\>**

  load custom UGENE settings file

- **--log-no-show-level**

  don't show message level at log

- **--log-no-show-date**

  don't show date&time info at log

- **--log-no-show-category**

  don't show message category at log

- **--log-level-trace**

  show trace log messages

- **--log-level-none**

  don't show log messages

- **--log-level-info**

  show error and info log messages (default)

- **--log-level-error**

  show only error log messages

- **--log-level-details**

  show details log messages

- **--log-color-output**

  colored output messages

- **--task-remote-machine=\<path-to-machine-file\>**

  run provided tasks on given remote machine

- **--ugene-stay-alive**

  do not stop ugene after finishing given tasks

- **--transl=\<language-code\>**

  load translations of specified language. Language is specified as a two-letter ISO 639 language code

## COMMANDS

- **UGENE** has commands for most significant features. Commands can be run as

  **ugene** \<command-name\> \[command-arguments\]

  **ugene** --task=\<command-name\> \[command-arguments\]

  See help for each command running **ugene** --help=\<command-name\>.

  List of available commands can be dumped using **ugene** --help.

## BUGS

If you find a bug, please report it at ugene@unipro.ru.

## AUTHOR

**ugene** was created by Unipro (http://unipro.ru)