bug report: codeml runmode = - 2 cleandata = 0 does not work as expected.

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Hongru Wang

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Apr 18, 2020, 4:16:48 PM4/18/20

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codeml runmode = - 2 cleandata = 0 does not work as expected. It generates the same results with that of cleandata = 1, which deletes all the data across all the gaps, not in a pairwise fashion.

Ziheng

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Jul 12, 2020, 4:47:07 AM7/12/20

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Yes, the program has been like that for some time. i think this is mentioned in pamlDOC.pdf.

if you want pairwise deletion, you will have to write some script, for example, to create a data file for each pair of sequences.