List Positions Matching Criteria

Background about lists

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

Purpose of listing positions

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.

How to list positions from a table

Command line for listing positions

Suppose you have already run seismic table:

seismic table out/sample/*/ref/sect

You can list the positions meeting certain criteria with

seismic +listpos out/sample/table/ref/sect

This command will output one list file for each table file, with the same path except table/ is replaced by list/.

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.