---
name: "alifmt"
section: "5"
platform: "linux"
package: "squizz"
version: "0.99d+dfsg-3"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/alifmt"
---

# alifmt(5)

Aligned sequences formats" 4

## NAME

alifmt - Aligned sequences formats" 4

## DESCRIPTION

This document illustrates some common formats used for aligned sequences representation.

- **CLUSTAL**

  ```
   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.

- **FASTA**

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

- **MEGA**

  ```
   #mega
   !Title Multiple Sequence Alignment;
   #MALK_ECOLI
   MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
   GLETITSGDLACRRLHKEPGV
   #MALK_SALTY
   MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
   GLETITSGDLACRRLHQEPGV
   #MALK_ENTAE
   MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
   GLETVTSGDL-----------
   #MALK_PHOLU
   MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------
   ---------------------
  ```

- **MSF**

  ```
   !!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.

- **NEXUS**

  ```
   #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.

- **PHYLIP**

  Sequential (PHYLIPS):

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

  Interleaved (PHYLIPI):

  ```
        2   109
   ATISA1    GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENND
   POTISA1   GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKD
             GENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMG
             GENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMG
             DEYGHTKGGN---
             DEYGHTKGGN---
  ```

  **Warning**: Species names may not contain characters \`( ) : ; , \[ \]' and exceed 10 characters.

- **STOCKHOLM**

  ```
   # 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  ---------------------
   //
  ```

## SEE ALSO

- [**squizz**(1)](/squizz/1.md), [**seqfmt**(5)](/seqfmt/5.md)

  ## AUTHOR

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