2.0

README.md

@@ -133,12 +133,12 @@ Launch _JolyTree_ without option to read the following documentation:
 * The option `-c` allows multiple substitutions per character to be accurately estimated when an observed _p_-distance is quite large (e.g. > 0.1; see [Figure 3.1](https://books.google.fr/books?id=3Xc8DwAAQBAJ&pg=PA41) in Nei and Kumar 2000). In such cases, all the _p_-distances _p_ estimated by _mash_ are transformed into proper evolutionary distances _d_. Since _JolyTree_ v2.0, four _p_-distance transformations can be obtained using options `-c` and/or `-a`:
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-| correction       | formula                                                                 | options                                                       | notes                                                                                             |
-|:-----------------|:------------------------------------------------------------------------|:--------------------------------------------------------------|:--------------------------------------------------------------------------------------------------|
-| none             | _d_ = _p_                                                               | `-c 1 -a $a` with any `$a` > 0                                | unaccurate estimate when _p_ > 0.1                                                                |
-| Poisson          | _d_ = - log<sub>_e_</sub>(1 - _p_)                                      | `-a 0` (use `-c 1` to force Poisson correction)               | default _p_-distance transformation of _mash_                                                     |
-| F81/EI           | _d_ = -_b_<sub>1</sub> log<sub>_e_</sub>(1 - _p_/_b_<sub>2</sub>)       | `-a 0` (use `-c 0` to force F81/EI correction)                | formula (4) in [Tamura and Kumar (2002)](https://academic.oup.com/mbe/article/19/10/1727/1258975) |
-| F81/EI + &Gamma; | _d_ = -_ab_<sub>1</sub>[(1 - _p_/_b_<sub>2</sub>)<sup>-1/_a_</sup> - 1] | `-a $a` with specified &Gamma; shape parameter (default: 1.5) | formula (3) in Criscuolo (2020; _submitted_)                                                      |
+| correction       | formula                                                                 | options                                               | notes                                                                                             |
+|:-----------------|:------------------------------------------------------------------------|:------------------------------------------------------|:--------------------------------------------------------------------------------------------------|
+| none             | _d_ = _p_                                                               | `-c 1 -a $a` with any `$a` > 0                        | unaccurate estimate when _p_ > 0.1                                                                |
+| Poisson          | _d_ = - log<sub>_e_</sub>(1 - _p_)                                      | `-a 0` (use `-c 1` to force Poisson correction)       | default transformation of _mash_                                                                  |
+| F81/EI           | _d_ = -_b_<sub>1</sub> log<sub>_e_</sub>(1 - _p_/_b_<sub>2</sub>)       | `-a 0` (use `-c 0` to force F81/EI correction)        | formula (4) in [Tamura and Kumar (2002)](https://academic.oup.com/mbe/article/19/10/1727/1258975) |
+| F81/EI + &Gamma; | _d_ = -_ab_<sub>1</sub>[(1 - _p_/_b_<sub>2</sub>)<sup>-1/_a_</sup> - 1] | `-a $a` to set &Gamma; shape parameter (default: 1.5) | formula (3) in Criscuolo (2020; _submitted_)                                                      |
 
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