ALIFMT(5)

💖 ALIFMT(5) — aligned sequence formats, but make it fashion 💖

okay so bestie, welcome to alifmt(5) from the User Manuals set 🫶 this page is literally just a lil tour of all the common ways people write down aligned sequences. no big life-changing flags, no options, just vibes and file formats. let's go ✨

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🌸 NAME 🌸

alifmt - Aligned sequences formats" 4

and yes, that stray " and that 4 are literally in the original, I'm not out here being chaotic on purpose 💀

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✨ DESCRIPTION ✨

This document illustrates some common formats used for aligned sequences representation. That's it, that's the whole assignment 💅 but there's a LOT of them, so buckle up.

🧬 CLUSTAL

It's giving classic. You get a lil header line, then names on the left with their sequences padded out next to them, and a lil * line chilling underneath. Behold:

CLUSTAL W (1.82) multiple sequence alignment

MALK_ECOLI      MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTL
MALK_SALTY      MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTL
MALK_ENTAE      MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTL
MALK_PHOLU      MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------
                *:** *:**:**:*:.::**:***:*::***

MALK_ECOLI      LRMIAGLETITSGDLACRRLHKEPGV
MALK_SALTY      LRMIAGLETITSGDLACRRLHQEPGV
MALK_ENTAE      LRMIAGLETVTSGDL-----------
MALK_PHOLU      LRM-----------------------
                ***

🚨 Warning: Names must not contain spaces or exceed 30 characters. not 31. thirty. the limit is real bestie 😭

🌈 FASTA

the people's format fr fr. each sequence gets a > header line with the name, and then the sequence wraps underneath:

>MALK_ECOLI
MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
GLETITSGDLACRRLHKEPGV
>MALK_SALTY
MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
GLETITSGDLACRRLHQEPGV
>MALK_ENTAE
MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
GLETVTSGDL-----------
>MALK_PHOLU
MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------LRM--
---------------------

no warnings, no drama, just a clean lil icon 🌸

🦋 MEGA

very MEGA of it. opens with a #mega line and a !Title line, then every name is prefixed with a #:

#mega
!Title Multiple Sequence Alignment;

#MALK_ECOLI
MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
GLETITSGDLACRRLHKEPGV
#MALK_SALTY
MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
GLETITSGDLACRRLHQEPGV
#MALK_ENTAE
MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
GLETVTSGDL-----------
#MALK_PHOLU
MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------
---------------------

🎀 MSF

okay this one is highkey extra and I respect it 👑 it's got a whole header, a PileUp of: line, a stats line, individual Name: lines with Len:, Check: and Weight:, then a //, then the actual numbered alignment blocks:

!!AA_MULTIPLE_ALIGNMENT 1.0
PileUp of: @pep.list

 msf.seq       MSF: 55  Type: P  Nov 22, 2001 11:02  Check: 2529 ..

 Name: m73237           Len:   655  Check: 7493  Weight:  1.00
 Name: l28824           Len:   655  Check: 5456  Weight:  1.00
 Name: u04379           Len:   655  Check: 9580  Weight:  1.00

//

        1                                                   50
m73237  ~~~~~MADSA NHLPFFFGQI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
l28824  MASSGMADSA NHLPFFFGNI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
u04379  ~~~~~MPDPA AHLPFFYGSI SRAEAEEHLK LAGMADGLFL LRQCLRSLGG

        51
m73237  ~~~~~
l28824  ~~~~~
u04379  AACG*

🚨 Warning: This format cannot handle more than 500 sequences in a single alignment. 501? not happening bestie 💀

🔥 NEXUS

living its best block-structured life: #NEXUS, then begin data; … endblock;, with dimensions, format and matrix doing the heavy lifting:

#NEXUS

begin data;
  dimensions ntax=2 nchar=80;
  format datatype=Protein interleave gap=- missing='.';
  matrix
[           1                                               50]
btdDm       -------AQQQQHHLHMQQAQHH-----------LHLSH------QQAQQ
TSp1        --------------------AEH-----------PSLR--------GTPL

[           51                          80]
btdDm       YACPICSKKFSRSDHLSKHKKTHF------
TSp1        FACPICNKRFMRSDHLAKHVKTHN------

    ;
endblock;

🚨 Warning: Text enclosed in brackets is considered as comment, and thus ignored. so those [...] lines? decoration only, bestie, the parser is skipping right past them 🫣

💜 PHYLIP

two flavors, pick your fighter. first up, Sequential (PHYLIPS) — each sequence gets to finish its whole thought before the next one starts:

     2   109
ATISA1    GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENNDG
          ENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMGDE
          YGHTKGGN---
POTISA1   GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKDG
          ENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMGDE
          YGHTKGGN---

and then Interleaved (PHYLIPI) — everybody takes turns, block by block, very group-project energy:

     2   109
ATISA1    GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENND
POTISA1   GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKD

          GENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMG
          GENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMG

          DEYGHTKGGN---
          DEYGHTKGGN---

🚨 Warning: Species names may not contain characters ( ) : ; , [ ]' and exceed 10 characters. yes I'm quoting it exactly like that, and yes, it really does say that 😭

🧚 STOCKHOLM

clean, minimal, iconic — header, name-plus-sequence columns, blank line, second block, and a // to close it out:

# STOCKHOLM 1.0

MALK_ECOLI  MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
MALK_SALTY  MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
MALK_ENTAE  MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
MALK_PHOLU  MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------

MALK_ECOLI  RCHLFREDGTACRRLHKEPGV
MALK_SALTY  RCHLFREDGSACRRLHQEPGV
MALK_ENTAE  ---------------------
MALK_PHOLU  ---------------------
//

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👀 SEE ALSO 👀

• squizz(1)
• seqfmt(5)

go read those next, they're the supporting cast and they ate 💅

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👑 AUTHOR 👑

Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.

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and that's the whole page bestie, we made it 🌈 this was ALIFMT(5) from the Unix collection, dated 2013-03-29 — go forth and align your sequences, you absolute icon 🫶💖✨