UGENE Command Line Interface

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

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

To use the UGENE CLI, ensure that you add the path to the UGENE executable to your %PATH% environment variable.

The general syntax is as follows:

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

Here:

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

task_parameter — A parameter of the specified task. Some parameters of a task are required, such as the 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

• CLI Options
• CLI Predefined Tasks
  • Format Converting Sequences
  • Converting MSA
  • Extracting Sequence
  • Finding ORFs
  • Finding Repeats
  • Finding Patterns Using the Smith-Waterman Algorithm
  • Adding Phred Quality Scores to Sequence
  • Local BLAST Search
  • Remote NCBI BLAST and CDD Requests
  • Annotating Sequence with UQL Schema
  • Building Profile HMM Using HMMER2
  • Searching HMM Signals Using HMMER2
  • Aligning with MUSCLE
  • Aligning with ClustalW
  • Aligning with ClustalO
  • Aligning with Kalign
  • Aligning with MAFFT
  • Aligning with T-Coffee
  • Building PFM
  • Searching for TFBS with PFM
  • Building PWM
  • Searching for TFBS with Weight Matrices
  • Building Statistical Profile for SITECON
  • Searching for TFBS with SITECON
  • Fetching Sequence from Remote Database
  • Gene-by-Gene Report
  • Reverse-Complement Converting Sequences
  • Variants Calling
  • Generating DNA Sequence
• Creating Custom CLI Tasks