• Name: Pete Klosterman
• Login Name: pete
• Email: PSKlosterman at lbl.gov
• Phone:
• Department:
• Location: Berkeley
• Comment: went to work at Affymetrix, September 2005

Project

• Enhance Ian's xrate evolutionary substitution rate matrices program (part of the DART package) to support asymmetric rate matrices. Thanks to Gerton Lunter for an implementation of general (real) matrix exponentiation.
  • For more information on matrix exponentiation:
    • Moler and Van Loan's classic "Nineteen Dubious Ways to Compute the Exponential of a Matrix": siam.org or EE221A notes
    • 2003 revisiting of "Dubious Ways"
    • Expokit
• Gerton's matrix exponentiation code has been tested extensively. It is quite accurate, agreeing with an extensive Taylor expansion to less than 1.0e-14; we have identified cases in which Gerton's code appears to behave well and the Taylor expansion diverges. Gerton's code has also been exercised in the context of the DART Xrate Program. A small test facility, Matrix Exponentiation Test, compares matrix exponentiation, using eigenvalues and eigenvectors, invoking Gerton's code, with that using eigenvalues and eigenvectors calculated using Robert Davies' implementation of Jacobi's method.
• This code is now used by xgram.

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