NAME

       alifmt - Aligned sequences formats

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), seqfmt(5)

AUTHOR

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