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given the similarity relation between $A$ and $B$ matrices;

$ A = L^{-1} B L $

if $A$ and $B$ are given, what is the best way to compute the similarity transformation matrix $L$?

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    The matrix $L$ need not be unique. One method is to find a "canonical form" for $A$ and $B$, which should be equal up to some easy permutation of blocks (e.g., the rational canonical form). If $R_A = R_B$, and $\beta$ is a rational canonical basis for $A$, $\gamma$ a rational canonical basis for $B$, then letting $P$ be the change-of-basis matrix for $\beta$ and $Q$ the change-of-basis matrix for $\gamma$, you get $Q^{-1}AQ = P^{-1}BP$, from whence you get $A = (QP^{-1})B(QP^{-1})^{-1}$.2011-10-26

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Answering the unanswered before it gets too old to be pushed to the front page. One possible answer is already given by Arturo Magidin in the comment.

If $A$ and $B$ are similar then they are also similar to a canonical form (typically the Jordan form). Thus, one way to find the similarity matrix is to reach to the canonical form, say $J$, from both matrices via $Q^{-1}AQ = J = P^{-1}BP$

Then, one can use either $A = (QP^{-1})B(QP^{-1})^{-1}$ or $B = (PQ^{-1})A(PQ^{-1})^{-1}$

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    Naw, I'm fine with it as a comment. :) (The first upvote's mine.)2011-11-06