What about Dennis Madsen et al's "Indonesia"?

http://xray.bmc.uu.se/dennis/

I don't think it's been updated in years (or I have a old link), but it's still quite nice as it runs locally using java.

AGS

> Date: Tue, 4 Mar 2008 12:02:20 -0800
> From: [log in to unmask]
> Subject: Re: [ccp4bb] multiple sequence alignment from multiple pairwise structural alignments
> To: [log in to unmask]
>
> On Tuesday 04 March 2008 11:13, Stephen Graham wrote:
> > Hi all,
> >
> > I would like to generate a structure-based multiple sequence alignment
> > using 4 structures. I have already generated pairwise alignments for
> > each 'pair' of structures (6 alignments in all). Is there a program
> > out there that can take a number of aligned structures (or even just a
> > number of pairwise sequence alignments) and calculate the 'best'
> > multiple sequence alignment? Please note that there is absolutely no
> > sequence conservation between these structures, making standard
> > sequence-based alignment tools pretty useless.
>
> My preference is for the CE-MC server. There are several sites that
> offer this, or you can install it locally. Here's one:
> bioinformatics.albany.edu/~cemc
>
> Another one is Tcoffee:
> http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi
>
> When I've done head-to-head comparisons, I have found the output from
> CE-MC to be preferable. In particular, in cases where you have two
> structures A and B that have the same length but have an area in which
> the structures differ, CE-MC will favor the alignment
> AAAAAAaaa...AAAA
> BBBBBB...bbbBBBB
> whereas Tcoffee will report
> AAAAAAaaaAAAA
> BBBBBBbbbBBBB
>
> For my purposes, the first is correct, even if aaa and bbb are
> sequence-homologous.
>
>
> --
> Ethan A Merritt Courier Deliveries: 1959 NE Pacific
> Dept of Biochemistry
> Health Sciences Building
> University of Washington - Seattle WA 98195-7742

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