RNAPLOT(1)

📦
version 2.7.0 · 5 versions
, in ubuntu resolute, ubuntu stonking

🦋 RNAPLOT(1) 🦋

Okay bestie, this is the RNAPLOT(1) page from the User Commands section, and it's giving main character energy 💅✨

✨ NAME ✨

RNAplot - manual page for RNAplot 2.7.0 🌸

✨ SYNOPSIS ✨

RNAplot [OPTIONS] [<input0>] [<input1>]...

Basically you call RNAplot, toss in some options if you want, and feed it as many input files as you like 🧚

✨ DESCRIPTION ✨

RNAplot 2.7.0 💖

Draw RNA Secondary Structures 🎀

Okay so RNAplot reads (aligned) RNA sequences and structures in the format that RNAfold or Stockholm 1.0 produces, then draws the secondary structure graph for you 🦋 The coordinates for those graphs come from either E. Bruccoleri's naview routines or a simple radial layout method. For aligned sequences and consensus structures (the --msa option), the graph can get annotated with covariance info 👀

It also makes a color-annotated EPS alignment figure, kinda like what RNAalifold and RNALalifold give you, which is so cute 🌈

Now the naming. If the sequence had a FASTA header, or the multiple sequence alignment has an ID field, those IDs become the names for your output file(s): "name_ss.ps" and "name_aln.ps". If not, you get "rna.ps" and "aln.ps" ✨ You can overrule all of that by explicitly setting a filename prefix with the --auto-id option. Heads up though: existing files with the same name get overwritten 💀

  • -h, --help — Print help and exit 🙌
  • --detailed-help — Print help, including all the details and hidden options, and exit 🔥
  • --full-help — Print help, including hidden options, and exit 🧚
  • -V, --version — Print version and exit 🌸
  • -v, --verbose — Be verbose. (default=off) Lower the log level setting so even INFO messages get passed through 🦋

🎀 I/O Options

Command line options for input and output (pre-)processing 💅

  • -i, --infile=<filename> — Read a file instead of reading from stdin. By default RNAplot reads input from stdin or from the file(s) that follow the RNAplot command. With this parameter you can name the input file(s) to read data from. Note, any additional files you supply to RNAplot still get processed too 🫶
  • -a, --msa — Input is a multiple sequence alignment in Stockholm 1.0 format. (default=off) Use this flag when your input is an MSA instead of single sequence(s). Note, only STOCKHOLM format lets you specify a consensus structure, so it's the only supported MSA format for now! 😭
  • --mis — Output "most informative sequence" instead of the simple consensus. (default=off) For each column of the alignment, this is the set of nucleotides with frequency greater than average, written in IUPAC notation 🍓
  • -j, --jobs[=number] — Split batch input into jobs and start processing in parallel using multiple threads. (default=0) Default processing is serial, one sequence at a time. With this switch, RNAplot creates as many parallel computation slots as you specify and assigns the input sequences from the input file(s) to the available slots. Note, this increases memory consumption, since input alignments have to stay in memory until an empty compute slot is free and each running job needs its own dynamic programming matrices. A value of 0 means use as many parallel threads as there are computation cores available ⚡
  • -f, --output-format=format — Specify the output file format. (possible values="eps", "svg", "gml", "xrna", "ssv" default=eps) Available formats are Encapsulated PostScript ('eps'), Scalable Vector Graphics ('svg'), Graph Meta Language ('gml'), and XRNA save file ('xrna'). Output filenames will end in ".eps", ".gml", ".svg", ".ss", respectively 🦋
  • --pre=string — Add annotation macros to the postscript file, and add the postscript code in "string" just before the code that draws the structure. This is an easy way to add annotation ✨
  • --post=string — Same vibe as --pre, but this one does NOT add the annotation macros. E.g. to mark position 15 with a circle, use --post="15 cmark" 🎯
  • --auto-id — Automatically generate an ID for each sequence. (default=off) The default mode of RNAfold is to automatically determine an ID from the input sequence data if the input file format allows it. Sequence IDs are usually given in the FASTA header of input sequences. If this flag is active, RNAfold ignores any IDs retrieved from the input and automatically generates one for each sequence. That ID is a prefix plus an increasing number. This flag can also be used to add a FASTA header to the output, even if the input has none 🪄
  • --id-prefix=STRING — Prefix for automatically generated IDs (as used in output file names). (default=sequence) If this parameter is set, each sequence gets prefixed with the provided string, so the output files follow the naming scheme "prefix_xxxx_ss.ps" (secondary structure plot), "prefix_xxxx_dp.ps" (dot-plot), "prefix_xxxx_dp2.ps" (stack probabilities), etc., where xxxx is the sequence number. Note: setting this parameter implies --auto-id 💜
  • --id-delim=CHAR — Change the delimiter between the prefix and the increasing number for automatically generated IDs (as used in output file names). (default=_) This lets you swap out the default "_" between the prefix string and the increasing number 🌈
  • --id-digits=INT — Specify the number of digits of the counter in automatically generated alignment IDs. (default=4) When alignment IDs are automatically generated, they get an increasing number starting at 1. That number is always left-padded with leading zeros so it takes up a set width, and this parameter lets you pick that width. We allow numbers in the range [1:18]. This option implies --auto-id 🔢
  • --id-start=LONG — Specify the first number in automatically generated IDs. (default=1) When sequence IDs are automatically generated, they get an increasing number, usually starting at 1. Use this parameter to set your own starting number. Note: negative numbers are not allowed. Note: setting this parameter means ignoring any IDs retrieved from the input data, i.e. it activates the --auto-id flag 🙈
  • --filename-delim=CHAR — Change the delimiting character used in sanitized filenames. (default=ID-delimiter) This is used while sanitizing filenames, i.e. replacing invalid characters. Note, the default delimiter ALWAYS is the first character of the "ID delimiter" you supply through the --id-delim option. If the delimiter is a whitespace character or empty, invalid characters are simply removed rather than substituted. Right now, these characters count as illegal in filenames: backslash \, slash /, question mark ?, percent sign %, asterisk *, colon :, pipe symbol |, double quote ", and triangular brackets < and > 🚫
  • --filename-full — Use the full FASTA header to create filenames. (default=off) This deactivates the default behavior of limiting output filenames to the first word of the sequence ID. Say an input has the FASTA header '>NM_0001 Homo Sapiens some gene'. Usually that produces output files with the prefix "NM_0001" and none of the extra header data, e.g. "NM_0001_ss.ps" for secondary structure plots. With this flag set, nothing gets truncated, so output filenames get the full FASTA header data as their prefixes. Note, though, that invalid characters (such as whitespace) will be substituted by a delimiting character or simply removed (see also --filename-delim) 📁
  • --log-level=level — Set the log level threshold. (default=2) By default, log messages are filtered so only warnings (level 2) or errors (level 3) get printed. Higher values mean fewer messages. Log-level 5 turns off all messages, even errors and other critical info 🤫
  • --log-file[=filename] — Print log messages to a file instead of stderr. (default=RNAplot.log) 📝
  • --log-time — Include a time stamp in log messages. (default=off) ⏰
  • --log-call — Include the file and line of the log calling function. (default=off) 🔍

🌸 Plotting

Command line options for changing the default behavior of structure layout and pairing probability plots 🎨

  • --covar — Annotate covariance of base pairs in the consensus structure. (default=off) 🌈
  • --covar-threshold=FLOAT — Set the threshold of maximum counter examples for coloring the consensus structure plot. (default=2) Floating point numbers between 0 and 1 are treated as frequencies among all sequences in the alignment. Everything else gets truncated to an integer and used as an absolute number of counter examples 🔥
  • --covar-min-sat=FLOAT — Set the minimum saturation for coloring the consensus structure plot. (default=0.2) This is a floating point number >= 0 and smaller than 1 💜
  • --aln — Produce a colored and structure annotated alignment in PostScript format, in the file "aln.ps" in the current directory. (default=off) 🖼️
  • --aln-EPS-cols=INT — Number of columns in the colored EPS alignment output. (default=60) A value less than 1 means the output doesn't get wrapped at all 📏
  • -t, --layout-type=INT — Choose the plotting layout algorithm. (possible values="0", "1", "2", "3", "4" default=1) This selects the layout algorithm that computes the nucleotide coordinates. Currently, the following algorithms are available:
    • '0': simple radial layout 🌼
    • '1': Naview layout (Bruccoleri et al. 1988) 🦋
    • '2': circular layout ⭕

Okay bestie, the list keeps going 💅

  • '3' — RNAturtle (Wiegreffe et al. 2018) 🐢
  • '4' — RNApuzzler (Wiegreffe et al. 2018) 🧩

✨ OPTIONS ✨ (continued)

  • --noOptimization — Turns off the drawing space optimization for RNApuzzler. It's giving "no shortcuts today" 🙈 (default=off)
  • --ignoreExteriorIntersections — Tells it to ignore intersections with the exterior loop inside the RNA-tree. Lowkey useful when the outer loop is being extra 🌸 (default=off)
  • --ignoreAncestorIntersections — Ignores ancestor intersections inside the RNA-tree. Not every overlap is a crisis, babe 💖 (default=off)
  • --ignoreSiblingIntersections — Ignores sibling intersections inside the RNA-tree. Sibling drama? Ignored 🙄✨ (default=off)
  • --allowFlipping — Lets exterior loop branches get flipped to sort out exterior branch intersections. Main character glow-up energy 🦋 (default=off)

✨ REFERENCES ✨

Okay, if you use this program in your work, you might wanna cite these lovelies 🎀

  • R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology: 6:26 📚
  • I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994), "Fast Folding and Comparison of RNA Secondary Structures", Monatshefte f. Chemie: 125, pp 167-188 🌈
  • R. Lorenz, I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and soft constraints", Algorithms for Molecular Biology 11:1 pp 1-13 💜

The energy parameters are taken from these queens 👑

  • D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker, D.H. Turner (2004), "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292 ⭐
  • D.H Turner, D.H. Mathews (2009), "NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure", Nucleic Acids Research: 38, pp 280-282 🍓

🎀 AUTHOR 🎀

The icons behind this are Ivo L Hofacker and Ronny Lorenz 🫶

🐛 REPORTING BUGS 🐛

If in doubt our program is right, nature is at fault. 💀

If something's off, send your comments to rna@tbi.univie.ac.at 📬

Bestie, that's the whole page! 🧚 This is RNAplot 2.7.0 from February 2026, and I'm obsessed with how it all came together 💅✨ Stay iconic and keep folding those structures 🌸🦋

📦 where this page comes from