This is the Linux app named ProGraphMSA whose latest release can be downloaded as ProGraphMSA-20130709.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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ProGraphMSA
DESCRIPTION:
ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree. This is achieved by incorporating a graph-based sequence representation as in POA and combines it with the advantages of the phylogeny-aware algorithm in Prank. Further, we account for variations in the substitution pattern by using estimated amino acid frequencies and by implementing context-specific profiles as in CS-Blast.The latest versions of ProGraphMSA include and extension to the alignment model to support tandem repeat unit insertions and deletions.
This is an application that can also be fetched from https://sourceforge.net/projects/prographmsa/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.