[Bioperl-l] how to change align output format

[江 文恺]

Dear all:

I have problems in changing the output format of clustal alignment.
I use the Bio::Tools::Run::Alignment::Clustalw module to carry out an 
mulitple sequences alignment, then i use the Bio::AlignIO module to write 
out the alignment. Scripts like this:
my 
$aln_out=Bio::AlignIO->new(-file=>">./clustal/${outfilename}.aln",-format=>'clustalw');

The output :
dana_GLEANR_16071      
MSKMKMLPVQLSLNQLNPGIWSDVLWRCPPAPSSQLAELKTQLPPSLPSDPRLWSREDVL
dere_GLEANR_9270       
..............S.............................................
FBgn0000097            
..............S.............................................
dsec_GLEANR_671        
..............S.............................................
dsim_GLEANR_6613       
..............S.............................................
dyak_GLEANR_1669       
..............S.............................................
                                     .


dana_GLEANR_16071      
VFLRFCVREFDLPKLDFDLFQMNGKALCLLTRADFGHRCPGAGDVLHNVLQMLIIESHMM
dere_GLEANR_9270       
............................................................
FBgn0000097            
............................................................
dsec_GLEANR_671        
............................................................
dsim_GLEANR_6613       
............................................................
dyak_GLEANR_1669       
............................................................

But , I want to change the output format as below, which do not change the 
identical residues into "." character. 
dere_GLEANR_9270       
MSKMKMLPVQLSLNSLNPGIWSDVLWRCPPAPSSQLAELKTQLPPSLPSDPRLWSREDVL
dyak_GLEANR_1669       
MSKMKMLPVQLSLNSLNPGIWSDVLWRCPPAPSSQLAELKTQLPPSLPSDPRLWSREDVL
dsec_GLEANR_671        
MSKMKMLPVQLSLNSLNPGIWSDVLWRCPPAPSSQLAELKTQLPPSLPSDPRLWSREDVL
dsim_GLEANR_6613       
MSKMKMLPVQLSLNSLNPGIWSDVLWRCPPAPSSQLAELKTQLPPSLPSDPRLWSREDVL
FBgn0000097            
MSKMKMLPVQLSLNSLNPGIWSDVLWRCPPAPSSQLAELKTQLPPSLPSDPRLWSREDVL
dana_GLEANR_16071      
MSKMKMLPVQLSLNQLNPGIWSDVLWRCPPAPSSQLAELKTQLPPSLPSDPRLWSREDVL
                       
**************.*********************************************

dere_GLEANR_9270       
VFLRFCVREFDLPKLDFDLFQMNGKALCLLTRADFGHRCPGAGDVLHNVLQMLIIESHMM
dyak_GLEANR_1669       
VFLRFCVREFDLPKLDFDLFQMNGKALCLLTRADFGHRCPGAGDVLHNVLQMLIIESHMM
dsec_GLEANR_671        
VFLRFCVREFDLPKLDFDLFQMNGKALCLLTRADFGHRCPGAGDVLHNVLQMLIIESHMM
dsim_GLEANR_6613       
VFLRFCVREFDLPKLDFDLFQMNGKALCLLTRADFGHRCPGAGDVLHNVLQMLIIESHMM
FBgn0000097            
VFLRFCVREFDLPKLDFDLFQMNGKALCLLTRADFGHRCPGAGDVLHNVLQMLIIESHMM
dana_GLEANR_16071      
VFLRFCVREFDLPKLDFDLFQMNGKALCLLTRADFGHRCPGAGDVLHNVLQMLIIESHMM
                       
************************************************************

Are their any parameters in the package that can be changed so that i can 
get the postier output format? Thank you Sincerely!

Jiang

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