Very large rDNA multiple sequence alignments

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Sat Feb 11 02:25:05 EST 2006

At present I am trying to perform multiple alignments of very large files
(<1000 sequences) of 16s rDNA from individuals within the same animal phyla.
I am finding that programs using the clustal platform cannot handle this.
The end application is not phylogenetic so I am relatively unconcerned about
ambiguous alignment within and around indels. Does anyone know of a program
that can handle alignments of this size in a windows operating system?


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