http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044431/
http://glee.ist.unomaha.edu:8080/seqmat/downloads.jsp
Most bioinformatics tools require specialized input formats for sequence comparison and analysis. This is particularly true for molecular phylogeny programs, which accept only certain formats. In addition, it is often necessary to eliminate highly similar sequences among the input, especially when the dataset islarge. Moreover, most programs have restrictions upon the sequence name. Here we introduce SeqMaT, a Sequence Manipulation Tool. It has the following functions:
data format conversion,
sequence name coding and decoding,
redundant and highly similar sequence removal, and
data mining utilities. SeqMaT was developed using Java with two versions, web-based andstandalone. A standalone program is convenient to manipulate a large number of sequences, while the web version will guarantee wide availability of the tool for researchers and practitioners throughout the Internet.
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