NEEDLEALL(1e)

💖 NEEDLEALL — the many-to-many alignment bestie 💖

okay so bestie, listen. this is the man page for needleall from the EMBOSS crew (that's the European Molecular Biology Open Software Suite, and yes it's giving very "acronym we made up at 2am" energy, but we love her). She lives in the Alignment:Global command group(s). Her whole thing? Many-to-many pairwise alignments of two sequence sets. Not one-to-one. MANY-to-many. she's an overachiever fr fr. 💅

---

✨ SYNOPSIS ✨

like this, exactly:

needleall -asequence seqset -bsequence seqall [-datafile matrixf]
          -gapopen float -gapextend float [-endweight boolean]
          [-endopen float] [-endextend float] [-minscore float]
          -brief boolean -outfile align [-errorfile outfile]

and also:

needleall -help

---

🌸 DESCRIPTION 🌸

needleall is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Alignment:Global" command group(s). she's a real one. no cap.

---

💅 OPTIONS 💅

🎀 Input section 🎀

• -asequence seqset — your first sequence set, bestie. slide it in here.
• -bsequence seqall — and this is the other one. the b to your a. the peanut butter to your jelly. 🫶
• -datafile matrixf — This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. so like, don't go renaming them, they live there. 👑

🔥 Required section 🔥

these ones are NOT optional. she said what she said.

• -gapopen float — The gap open penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default value: @($(acdprotein)? 10.0 : 10.0 )
• -gapextend float — The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Default value: @($(acdprotein)? 0.5 : 0.5 )

the vibe: gapopen is the "ouch, a gap appeared" tax, and gapextend is the "ouch, the gap got LONGER" tax. keep the second one smaller, that's the whole trick. 💀

🦋 Additional section 🦋

• -endweight boolean — Default value: N
• -endopen float — The end gap open penalty is the score taken away when an end gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default value: @($(acdprotein)? 10.0 : 10.0 )
• -endextend float — The end gap extension, penalty is added to the end gap penalty for each base or residue in the end gap. Default value: @($(acdprotein)? 0.5 : 0.5 )
• -minscore float — Minimum alignment score to report an alignment. if it doesn't clear the bar, it doesn't get a seat at the table, periodt. ✨

🌈 Output section 🌈

• -brief boolean — Brief identity and similarity Default value: Y
• -outfile align — where the alignments go. your moment. main character energy. 👑
• -errorfile outfile — Error file to be written to Default value: needleall.error

---

😭 BUGS 😭

Bugs can be reported to the Debian Bug Tracking system (<http://bugs.debian.org/emboss>), or directly to the EMBOSS developers (<http://sourceforge.net/tracker/?group_id=93650&atid=605031>). not me asking you to snitch on the bugs, but like, do snitch, they wanna know. 🙈

---

🧚 SEE ALSO 🧚

needleall is fully documented via the tfm(1) system. iykyk. 🍓

---

💜 AUTHOR 💜

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

• Wrote the script used to autogenerate this manual page. iconic behaviour honestly.

---

⭐ COPYRIGHT ⭐

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself. (yes that means the whole EMBOSS package's terms, no take-backs, we stan a clear license. 🌸)

---

and that's the whole page bestie!! 💖 this shipped as part of EMBOSS 6.4.0, dated 05/11/2012, and it's the NEEDLEALL(1e) page from the EMBOSS Manual for Debian. go forth and align many-to-many, you absolute legend. 🎀🦋✨