Tajima Relative Rate Test Of Molecular Clock
The script tests the hypothesis of a molecular evolutionary clock (i.e., a constant rate of molecular evolution) between two groups of sequences (DNA or Amino Acid) using an outgroup sample.
Usage: perl RelativeRateTest.pl [1.aln.fasta] [2.aln.fasta] [outgroup.aln.fasta] [output]
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The input sequences should be aligned and in fasta format (i.e. the *.aln.fasta files should have the same length). The script also does Holm–Bonferroni correction.
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If you want to run the relative rate test for clusters of species on a tree, please use LINTRE: http://www.kms.ac.jp/~genomelb/takezaki/lintre/index.html
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References:
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Tajima, F. (1993) Simple methods for testing molecular clock hypothesis. Genetics, 135, 599--607. (Equation 4)
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Holm, S. (1979). A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics. 6 (2): 65–70.