UGENE(1)

✨ UGENE — like, the whole integrated bioinformatics suite, bestie ✨

okay so this is the manual page for UGENE, living in the General Commands Manual section of your friendly neighborhood man pages. it's giving "one program to rule all your genomic data" and honestly? it kind of is. 🧬💖

🌸 NAME 🌸

UGENE — the integrated bioinformatics suite. that's it, that's the name, no notes. 💅

🦋 SYNOPSIS 🦋

ugene -ui

ugene [OPTIONS]

💜 DESCRIPTION 💜

UGENE is a cross-platform environment for DNA and protein sequence analysis. it pulls together the most popular bioinformatics computational algorithms and gives you both a GUI and a command line interface, so you can do complex analysis of genomic data however your little heart desires. main character energy, fr fr. ✨

here's the tea on what UGENE can do — the main features:

• 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

ngl, UGENE has a modular structure, and almost all of its functionality comes wrapped inside plugins. internally it's designed with support of parallelism so it can actually make profit from using multicore computers (yes, your 16-core machine is finally the main character). every computational task in UGENE is performed in background and does not block your interaction with the graphical interface. so you can keep vibing while it crunches. 🫶

🎀 OPTIONS 🎀

• -ui — run the GUI version of UGENE. the pretty one. the one with windows. 🪟✨
• --help — print a usage message briefly summarizing all command-line options plus the program version, then exit. cute, quick, informative.
• --license — dump license information. read your receipts bestie 💅
• --task=<path-to-schema or schema-name> [schema-options] — run a given workflow schema. yes you can feed it a path or a schema name, and yes it takes schema options too.
• --status-bar-hide — don't show the task status bar. minimalism era. 🙈
• --ini-file=<path-to-settings-file> — load a 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. the most yappy setting.
• --log-level-none — don't show log messages. silence, iconic, serene. 🤫
• --log-level-info — show error and info log messages (this is the default).
• --log-level-error — show only error log messages. dramatic but efficient.
• --log-level-details — show details log messages.
• --log-color-output — colored output messages 🌈 because plain text is lowkey sad.
• --task-remote-machine=<path-to-machine-file> — run provided tasks on a given remote machine. outsourcing, but make it science.
• --ugene-stay-alive — do not stop ugene after finishing given tasks. it simply refuses to leave the party. 💀
• --transl=<language-code> — load translations of a specified language. the language is specified as a two-letter ISO 639 language code.

🌟 COMMANDS 🌟

UGENE has commands for its most significant features. and the way you run them? two whole ways, bestie:

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

see help for each command by running ugene --help=<command-name>.

and if you wanna see the list of available commands, just dump it using ugene --help. iykyk. 💖

💀 BUGS 💀

if you find a bug, please report it at ugene@unipro.ru. do NOT suffer in silence, bestie, tell the devs. 🐛

⭐ AUTHOR ⭐

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

and that's the whole page!! this one's from the General Commands Manual, and it was last dated 11 February 2011 — yeah, vintage, but she still serves. take care of your sequences out there 🧚💜