JALVIEW(1)

💖 jalview — like, the multiple alignment editor, bestie 💖

okay so real quick: this is the manual page for jalview(1), from the General Commands Manual section. it's the whole vibe. let's go. ✨

🌸 NAME 🌸

jalview — Multiple alignment editor. that's it, that's the girl. she edits alignments. 👑

🦋 SYNOPSIS 🦋

jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]

✨ DESCRIPTION ✨

so Jalview provides facilities for viewing/editing and otherwise manipulating sequence alignments (DNA, amino acids). literally the whole point. she's giving main character energy for your alignments. 🧬💅

🎀 OPTIONS 🎀

okay bestie, here's every single flag, no skipping, fr fr:

• -nodisplay — run Jalview without User Interface. no window, just vibes. 🙈
• -props FILE — use the given Jalview properties file instead of users default. custom config, she's not like other girls. 📁
• -colour COLOURSCHEME — the colourscheme to be applied to the alignment. yes bestie, serve looks. 🌈
• -annotations FILE — add precalculated annotations to the alignment. receipts, already done. ✍️
• -tree FILE — load the given newick format tree file onto the alignment. family tree but make it science. 🌳
• -features FILE — use the given file to mark features on the alignment. highlighting, but professional. ⭐
• -fasta FILE — create alignment file FILE in Fasta format. 🍓
• -clustal FILE — create alignment file FILE in Clustal format. 💜
• -pfam FILE — create alignment file FILE in PFAM format. 🎀
• -msf FILE — create alignment file FILE in MSF format. 💖
• -pileup FILE — create alignment file FILE in Pileup format 🦋
• -pir FILE — create alignment file FILE in PIR format. ✨
• -blc FILE — create alignment file FILE in BLC format. 🌸
• -json FILE — create alignment file FILE in JSON format. 👑
• -jalview FILE — create alignment file FILE in Jalview format. the self-portrait, iconic. 💅
• -png FILE — create PNG image FILE from alignment. 📸
• -svg FILE — create SVG image FILE from alignment. crisp, scalable, gorgeous. 🌟
• -html FILE — create HTML file from alignment. 🕸️
• -biojsMSA FILE — create BioJS MSA Viewer HTML file from alignment. 🔬
• -imgMap FILE — create HTML file FILE with image map of PNG image. 🗺️
• -eps FILE — create EPS file FILE from alignment. 📐
• -questionnaire URL — queries the given URL for information about any Jalview user questionnaires. she's nosy but politely. 📝
• -noquestionnaire — turn off questionnaire check. not today, survey. 🚫
• -nonews — turn off check for Jalview news. no spoilers bestie. 📰
• -nohtmltemplates — disable the automatic download of templates in the Github repository. staying offline, respectfully. 📵
• -sortbytree OR -nosortbytree — enable or disable sorting of the given alignment by the given tree. pick a lane, both are valid. 🔀
• -jabaws URL — specify URL for Jabaws services (e.g. for a local installation). 🖥️
• -fetchfrom nickname — query nickname for features for the alignments and display them. 💌
• -groovy FILE — execute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN). she waits her turn, so polite. 🎭
• -jvmmempc=PERCENT — only available with standalone executable jar or jalview.bin.Launcher. limit maximum heap size (memory) to PERCENT percents of total physical memory detected. this defaults to 90 if total physical memory can be detected. see https://www.jalview.org/help/html/memory.html for more details. 🧠
• -jvmmemmax=MAXMEMORY — only available with standalone executable jar or jalview.bin.Launcher. limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). this defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. see https://www.jalview.org/help/html/memory.html for more details. 🔥

okay lowkey important: those last two memory flags are only available with the standalone executable jar or jalview.bin.Launcher. don't come for me if you try them elsewhere. 😭

🌈 SEE ALSO 🌈

• https://www.jalview.org

go look, it's cute over there. 🫶

💜 AUTHOR 💜

this manual page was written by Vincent Fourmond <fourmond@debian.org> and Pierre Gruet <pgt@debian.org> from the Debian project, but may be used by others. shoutout to the Debian girlies for the lore. 👑

and that's the whole page bestie!! dated 06-02-2021, and this is JALVIEW(1) — the one and only. mwah, slay, bye!! 💖✨🎀🦋🌸💅🫶