ClustalW multiple alignment format

From BioPerl

The CLUSTALW format (also CLUSTALV) is supported by most multiple alignment programs.

Thompson J.D., Higgins D.G., Gibson T.J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.

Example

CLUSTAL W (1.81) multiple sequence alignment

CYS1_DICDI      -----MKVILLFVLAVFTVFVSS---------------RGIPPEEQ------------SQ
ALEU_HORVU      MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALR
CATH_HUMAN      ------MWATLPLLCAGAWLLGV--------PVCGAAELSVNSLEK------------FH
                          * :*.. :  :.                 .  . *.             .

CYS1_DICDI      FLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE
ALEU_HORVU      FARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN----RKGLPYRLGINRFSDMSWEE
CATH_HUMAN      FKSWMSKHRKTY-STEEYHHRLQTFASNWRKINAHN----NGNHTFKMALNQFSDMSFAE
                *  :  .. *.* *  *   *:  * ..  ::   *    .     .:.:*.*:*:*  *

CYS1_DICDI      FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG-AVTPVKNQGQCGSCWSFS
ALEU_HORVU      FQATRL-GAAQTCSATLAGNHLMRDA--AALPETKDWREDG-IVSPVKNQAHCGSCWTFS
CATH_HUMAN      IKHKYLWSEPQNCSAT--KSNYLRGT--GPYPPSVDWRKKGNFVSPVKNQGACGSCWTFS
                ::   * .     :        : .    . * : ***  *  *:*****. *****:**

CYS1_DICDI      TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG
ALEU_HORVU      TTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNG
CATH_HUMAN      TTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY--------GCQGGLPSQAFEYILYNK
                *** :*.    : .* :**:**:****     ::        **:*** .:*::**  *  

CYS1_DICDI      GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KNETVMAGYIVSTGPLAIAADAV
ALEU_HORVU      GIDTEESYPYKGVNGV-CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVI
CATH_HUMAN      GIMGEDTYPYQGKDGY-CKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVT
                **  *.:*** .  *  *:::. :    : : . *.   *  :   :    *::.* :. 

CYS1_DICDI      E-WQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQG
ALEU_HORVU      DGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGV-----PYWLIKNSWGADWGDNG
CATH_HUMAN      QDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGI-----PYWIVKNSWGPQWGMNG
                : :  *  *:: .  *   *:.::*.:* ***. :* :     ***::*****.:** :*

CYS1_DICDI      YIYLRRGKNTCGVSNFVSTSII--
ALEU_HORVU      YFKMEMGKNMCAIATCASYPVVAA
CATH_HUMAN      YFLIERGKNMCGLAACASYPIPLV
                *: :  *** *.::  .* .: