how to judge the quality of a alignment when doing model building?

[Chyh-chong Chuang]

Dear netters:

	I am curious how to judge the quality of a alignment when doing 
model building? The alignment pattern direct the way to assign structure 
conserved region, but how to judge the quality? 
	Any comment will be appreciated.

Thanks all.

ccchuang

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    Chyh-Chong Chuang
    Institude of Biological Chemistry, 
    Academia Sinica,Taipei, Taiwan
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    Phone: 886-2-7858981 ext 7091 
    Fax: 886-2-7883473
    E-Mail: ccchuang at gate.sinica.edu.tw
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