ANCESCON

Ancestral sequence reconstruction

Reference: Reconstruction of ancestral protein sequences and its applications. Wei Cai, Jimin Pei, and Nick V. Grishin. BMC Evol Biol. 2004 Sep 17;4:33.
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OPTIONS: Ancestral sequence reconstruction:
    Reconstruct sequences for all internal nodes
    Reconstruct ancestral sequence only for the root (midpoint of the tree) (marginal reconstruction only)
    Reconstruct sequences for the root AND all internal nodes (marginal reconstruction only)

Reconstruction method:
    marginal reconstruction
    joint reconstruction

Parameters in ancestral sequence reconstruction:
    Rate factor
        Use alignment-based (AB) rate factor (less time than ML and higher precision than uniform)
        Use maximum likelihood (ML) rate factor (more time and higher precision than AB)
        Use uniform rate factor
    Gap content for rate factor calculation:
    PI vector:
        Use alignment-based PI vector
        Optimize PI vector with Powell method
        Optimize PI vector with Downhill Simplex Method in Multidimensions
        Optimize PI vector with Continuous Minimization by Simulated Annealing
        Optimize PI vector for each site with Continuous Minimization by Simulated Annealing

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Last modified: Wed Aug 16 15:10:00 CDT 2006