Commit 48898847 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: diversity measures, more explanations

parent 9376560c
......@@ -436,12 +436,14 @@ The first window has 8 occurrences, the second window has 5 occurrences.
** Diversity measures
Several [[https://en.wikipedia.org/wiki/Diversity_index][diversity indices]] indices are reported, both on the standard output and in the =.vidjil= file:
Several [[https://en.wikipedia.org/wiki/Diversity_index][diversity indices]] are reported, both on the standard output and in the =.vidjil= file:
- H (=index_H_entropy=): Shannon's diversity
- E (=index_E_equitability=): Shannon's equitability
- Ds (=index_Ds_diversity=): Simpson's diversity
E ans Ds values are between 0 (no diversity, one clone gathers all analyzed reads)
and 1 (full diversity, each analyzed read belongs to a different clone).
** Unsegmentation causes
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