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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

Free

TreeView is a program to view phylogenetic trees in your computer.

MEGA, and ClustalW/X) * supports standard ...MEGA, and ClustalW/X. Once loaded 

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BSEdit

Free

BSEdit is a WYSIWYG and efficient multiple sequence alignment editor.

BSEdit supports clustalW, Fasta, Phylip ...alignment. - Supports clustalW, Fasta, Phylip 

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GPMAW

Free

Is primarily intended as a tool for mass spectrometric analysis of proteins.

alignment using ClustalW 

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ClustalW2

Free

ClustalW2 is a general purpose multiple sequence alignment program for DNA.

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