Package Bio :: Package Phylo :: Package PAML :: Module _parse_yn00
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Module _parse_yn00

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Functions [hide private]
 
parse_ng86(lines, results)
Parse the Nei & Gojobori (1986) section of the results.
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parse_yn00(lines, results, sequences)
Parse the Yang & Nielsen (2000) part of the results.
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parse_others(lines, results, sequences)
Parse the results from the other methods.
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Variables [hide private]
  __package__ = 'Bio.Phylo.PAML'
Function Details [hide private]

parse_ng86(lines, results)

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Parse the Nei & Gojobori (1986) section of the results. Nei_Gojobori results are organized in a lower triangular matrix, with the sequence names labeling the rows and statistics in the format: w (dN dS) per column Example row (2 columns): 0.0000 (0.0000 0.0207) 0.0000 (0.0000 0.0421)

parse_yn00(lines, results, sequences)

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Parse the Yang & Nielsen (2000) part of the results. Yang & Nielsen results are organized in a table with each row comprising one pairwise species comparison. Rows are labeled by sequence number rather than by sequence name.

parse_others(lines, results, sequences)

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Parse the results from the other methods.

The remaining methods are grouped together. Statistics for all three are listed for each of the pairwise species comparisons, with each method's results on its own line. The stats in this section must be handled differently due to the possible presence of NaN values, which won't get caught by my typical "line_floats" method used above.