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List Positions Matching Criteria

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Background about lists

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You can use +listpos to list positions meeting specific criteria in tables.

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Purpose of listing positions

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After you run seismic table, you may want to find the positions that meet +certain criteria, such as the mutation rate being less/greater than a threshold.

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How to list positions from a table

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Command line for listing positions

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Suppose you have already run seismic table:

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seismic table out/sample/*/ref/sect
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You can list the positions meeting certain criteria with

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seismic +listpos out/sample/table/ref/sect
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This command will output one list file for each table file, with the same path +except table/ is replaced by list/.

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You can filter the positions using options such as --max-fmut-pos 0.01, +which will output all positions with a mutation rate of 0.01 or less. +Using --complement lists the complement of the positions; for example, +--complement --max-fmut-pos 0.01 would output all positions with a mutation +rate greater than 0.01.

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