**0**wrote:

Hello.

I have read the article "A* with Partial Expansion for large branching factor problems" [1] by T. Yoshizumi, T. Miura and T Ishida. Also, I came up with an implementation of their algorithm, and applied it to solving the multiple sequence alignment problem. The paper presents the PAM250 substitution matrix used for scoring the alignment, but they never stated what gap penalty value they used, but rather stated that the prior relevant research paper proposes the value of 8, which, in my program, results in alignment not matching the result of ClustalX on the same input.

What gap penalty value should I use in the context of [1]?