This documentation is for version 2.0.dev, which is not released yet.
Return the Percentage Identity (PID) score of the calculated MSA.
mode : { 1, 2, 3, 4, 5 }
Indicate which of the four possible PID scores described in Raghava2006 should be calculated, the fifth possibility is added for linguistic purposes: identical positions / (aligned positions + internal gap positions), identical positions / aligned positions, identical positions / shortest sequence, or identical positions / shortest sequence (including internal gap pos.) identical positions / (aligned positions + 2 * number of gaps)
Indicate which of the four possible PID scores described in Raghava2006 should be calculated, the fifth possibility is added for linguistic purposes:
score : float
The PID score of the given alignment as a floating point number between 0 and 1.
See also
lingpy.algorithm.misc.pid
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