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Stockholm University Palign RPC API - SDKs

ProteinALIGNment (Palign) is a protein sequence alignment service provided by Stockholm University that consists of a set of SOAP functions for resolving many types of alignment problems. It can align two sequences, a sequence and a structure, a sequence and a profile, or two profiles. Palign is not very well documented, but is freely available under a GPL-like license. While not the fastest of programs, it is very flexible.
Stockholm University Palign