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clustalx

Free

Clustal X is a windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results.
The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment.

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TreeView X

Free

reeView X is an open source program to display phylogenetic trees.

OS X, and Windows platforms. It ...by PAUP*, ClustalX, TREE-PUZZLE ...Classic and Windows 

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