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Program for estimating amino acid replacement rates

Project description

Usage: modelestimator <format> <options> infiles

<format> should be either FASTA, STOCKHOLM or PHYLIP
Output is a rate matrix and residue distribution vector.

Options:
-threshold or -t <f>
Stop when consecutive iterations do not change by more than <f>. Default is 0.001.
-bootstrap or -b <r>
Perform bootstrapping on multialignment with <r> resamplings. Only one infile should be given in this mode. Returns bootstrap norm.

Example usage:
modelestimator fasta -t 0.001 file1.fa file2.fa file3.fa
modelestimator fasta -b 200 file.fa

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