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.
Enter query sequences in
CLUSTAL
format:
Or file name:
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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
Input your own
tree file
:
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Last modified: Wed Aug 16 15:10:00 CDT 2006