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UGENE command line interface (CLI) was developed keeping in mind the following principles:

  • To make it as easy as popular shell commands.
  • To include all significant UGENE features.
  • To allow users to add their own commands.

To use UGENE CLI make sure to add the path to the UGENE executable to your %PATH% environment variable.

The general syntax is the following:

ugene [[--task=]task_name] [--task_parameter=value ...] [-task_parameter value ...] [--option[=value]] [-option[ value]]


task_name — task to execute, it can be one of the predefined tasks or a task you have created.

task_parameter — parameter of the specified task. Some parameters of a task are required, like in and out parameters of some tasks.

option — one of the CLI options.

See the example below:

ugene align --in=COI.aln -out result.aln -log-level-details

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