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.\" ========================================================================
.\"
.IX Title "ALIFMT 5"
.TH ALIFMT 5 "2009-05-19" "Unix" "User Manuals"
.SH "NAME"
.IP "\fBalifmt\fR \- Aligned sequences formats" 4
.IX Item "alifmt - Aligned sequences formats"
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This document illustrates some common formats used for aligned sequences
representation.
.IP "\fB\s-1CLUSTAL\s0\fR" 4
.IX Item "CLUSTAL"
.Vb 1
\& CLUSTAL W (1.82) multiple sequence alignment
.Ve
.Sp
.Vb 5
\& MALK_ECOLI      MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTL
\& MALK_SALTY      MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTL
\& MALK_ENTAE      MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTL
\& MALK_PHOLU      MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------
\&                 *:** *:**:**:*:.::**:***:*::***
.Ve
.Sp
.Vb 5
\& MALK_ECOLI      LRMIAGLETITSGDLACRRLHKEPGV
\& MALK_SALTY      LRMIAGLETITSGDLACRRLHQEPGV
\& MALK_ENTAE      LRMIAGLETVTSGDL-----------
\& MALK_PHOLU      LRM-----------------------
\&                 ***
.Ve
.Sp
\&\fBWarning\fR: Names must not contain spaces or exceed 30 characters.
.IP "\fB\s-1FASTA\s0\fR" 4
.IX Item "FASTA"
.Vb 12
\& >MALK_ECOLI
\& MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
\& GLETITSGDLACRRLHKEPGV
\& >MALK_SALTY
\& MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
\& GLETITSGDLACRRLHQEPGV
\& >MALK_ENTAE
\& MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
\& GLETVTSGDL-----------
\& >MALK_PHOLU
\& MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------LRM--
\& ---------------------
.Ve
.IP "\fB\s-1MEGA\s0\fR" 4
.IX Item "MEGA"
.Vb 2
\& #mega
\& !Title Multiple Sequence Alignment;
.Ve
.Sp
.Vb 12
\& #MALK_ECOLI
\& MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
\& GLETITSGDLACRRLHKEPGV
\& #MALK_SALTY
\& MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
\& GLETITSGDLACRRLHQEPGV
\& #MALK_ENTAE
\& MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
\& GLETVTSGDL-----------
\& #MALK_PHOLU
\& MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------
\& ---------------------
.Ve
.IP "\fB\s-1MSF\s0\fR" 4
.IX Item "MSF"
.Vb 2
\& !!AA_MULTIPLE_ALIGNMENT 1.0
\& PileUp of: @pep.list
.Ve
.Sp
.Vb 1
\&  msf.seq       MSF: 55  Type: P  Nov 22, 2001 11:02  Check: 2529 ..
.Ve
.Sp
.Vb 3
\&  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
.Ve
.Sp
.Vb 1
\& //
.Ve
.Sp
.Vb 4
\&         1                                                   50
\& m73237  ~~~~~MADSA NHLPFFFGQI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
\& l28824  MASSGMADSA NHLPFFFGNI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
\& u04379  ~~~~~MPDPA AHLPFFYGSI SRAEAEEHLK LAGMADGLFL LRQCLRSLGG
.Ve
.Sp
.Vb 4
\&         51
\& m73237  ~~~~~
\& l28824  ~~~~~
\& u04379  AACG*
.Ve
.Sp
\&\fBWarning\fR: This format cannot handle more than 500 sequences in a
single alignment.
.IP "\fB\s-1NEXUS\s0\fR" 4
.IX Item "NEXUS"
.Vb 1
\& #NEXUS
.Ve
.Sp
.Vb 7
\& begin data;
\&   dimensions ntax=2 nchar=89;
\&   format datatype=Protein interleave gap=- missing='.';
\&   matrix
\& [           1                                               50]
\& btdDm       -------AQQQQHHLHMQQAQHH-----------LHLSH------QQAQQ
\& TSp1        --------------------AEH-----------PSLR--------GTPL
.Ve
.Sp
.Vb 3
\& [           51                          80]
\& btdDm       YACPICSKKFSRSDHLSKHKKTHF------
\& TSp1        FACPICNKRFMRSDHLAKHVKTHN------
.Ve
.Sp
.Vb 2
\&     ;
\& endblock;
.Ve
.Sp
\&\fBWarning\fR: Text enclosed in brackets is considered as comment, and
thus ignored.
.IP "\fB\s-1PHYLIP\s0\fR" 4
.IX Item "PHYLIP"
Sequential (\s-1PHYLIPS\s0):
.Sp
.Vb 7
\&      2   109
\& ATISA1    GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENNDG
\&           ENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMGDE
\&           YGHTKGGN---
\& POTISA1   GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKDG
\&           ENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMGDE
\&           YGHTKGGN---
.Ve
.Sp
Interleaved (\s-1PHYLIPI\s0):
.Sp
.Vb 3
\&      2   109
\& ATISA1    GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENND
\& POTISA1   GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKD
.Ve
.Sp
.Vb 2
\&           GENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMG
\&           GENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMG
.Ve
.Sp
.Vb 2
\&           DEYGHTKGGN---
\&           DEYGHTKGGN---
.Ve
.Sp
\&\fBWarning\fR: Species names may not contain characters `( ) : ; , [ ]'
and exceed 10 characters.
.IP "\fB\s-1STOCKHOLM\s0\fR" 4
.IX Item "STOCKHOLM"
.Vb 1
\& # STOCKHOLM 1.0
.Ve
.Sp
.Vb 4
\& MALK_ECOLI  MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
\& MALK_SALTY  MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
\& MALK_ENTAE  MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
\& MALK_PHOLU  MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------
.Ve
.Sp
.Vb 5
\& MALK_ECOLI  RCHLFREDGTACRRLHKEPGV
\& MALK_SALTY  RCHLFREDGSACRRLHQEPGV
\& MALK_ENTAE  ---------------------
\& MALK_PHOLU  ---------------------
\& //
.Ve
.SH "SEE ALSO"
.IX Header "SEE ALSO"
.IP "\fBsquizz\fR(1), \fBseqfmt\fR(5)" 4
.IX Item "squizz(1), seqfmt(5)"
.SH "AUTHOR"
.IX Header "AUTHOR"
Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.