Description Usage Arguments Details Value Author(s) See Also Examples
Functions for highlighting sequences that may represent external (exCon
) or internal contamination (inCon
).
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DNAbin |
An object of class |
outlierLabels |
The format of displaying the labels of the outlying sequences. Three options are implemented: |
exCon
calculates the mean distances between sequences in the alignment, systematically leaving removing a single sequence.
inCon
creates a binary distance matrix that
exCon
plots the mean distance and 95% limits, and returns a list with the following elements:
means |
Mean distance of each of the jacknifed alignments. |
highCI |
Upper 95% limit. |
lowCI |
Lower 95% limit. |
above |
Index of sequences above the upper limit. |
below |
Index of sequences below the lower limit. |
inCon
returns a binary matrix with 0 indicating identical sequences.
Samuel Brown <s_d_j_brown@hotmail.com>
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