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  ---------------------
//