@@ -132,6 +132,7 @@ Launch _JolyTree_ without option to read the following documentation:
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@@ -132,6 +132,7 @@ 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`:
* 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`:
@@ -140,6 +141,7 @@ Launch _JolyTree_ without option to read the following documentation:
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@@ -140,6 +141,7 @@ Launch _JolyTree_ without option to read the following documentation:
| 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 | _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 + Γ | _d_ = -_ab_<sub>1</sub>[(1 - _p_/_b_<sub>2</sub>)<sup>-1/_a_</sup> - 1] | `-a $a` to set Γ shape parameter (default: 1.5) | formula (3) in Criscuolo (2020; _submitted_) |
| F81/EI + Γ | _d_ = -_ab_<sub>1</sub>[(1 - _p_/_b_<sub>2</sub>)<sup>-1/_a_</sup> - 1] | `-a $a` to set Γ shape parameter (default: 1.5) | formula (3) in Criscuolo (2020; _submitted_) |
</sub>
</div>
</div>
* The F81 corrections estimate pairwise distances based on the Equal-Input (EI) model of nucleotide substitution ([Felsenstein 1981](https://link.springer.com/article/10.1007/BF01734359); [Tajima and Nei 1982](https://link.springer.com/article/10.1007/BF01810830), [1984](https://academic.oup.com/mbe/article/1/3/269/1244029), [Tamura and Kumar 2002](https://academic.oup.com/mbe/article/19/10/1727/1258975)). These transformations were chosen because they can be directly computed from _p_-distances, and take into account putative unequal base frequencies and heterogeneous base composition among lineages (option `-f`; for details about the values _b_<sub>1</sub> and _b_<sub>2</sub>, see e.g. [Tamura and Kumar 2002](https://academic.oup.com/mbe/article/19/10/1727/1258975), [Criscuolo 2019](https://riojournal.com/article/36178/)). Thanks to the use of the supplementary gamma shape parameter (option `-a`), F81/EI gamma distance allows approximating evolutionary distances derived from complex nucleotide substitution models (the default parameter _a_ = 1.5 enables pairwise distances to be conveniently estimated in many cases).
* The F81 corrections estimate pairwise distances based on the Equal-Input (EI) model of nucleotide substitution ([Felsenstein 1981](https://link.springer.com/article/10.1007/BF01734359); [Tajima and Nei 1982](https://link.springer.com/article/10.1007/BF01810830), [1984](https://academic.oup.com/mbe/article/1/3/269/1244029), [Tamura and Kumar 2002](https://academic.oup.com/mbe/article/19/10/1727/1258975)). These transformations were chosen because they can be directly computed from _p_-distances, and take into account putative unequal base frequencies and heterogeneous base composition among lineages (option `-f`; for details about the values _b_<sub>1</sub> and _b_<sub>2</sub>, see e.g. [Tamura and Kumar 2002](https://academic.oup.com/mbe/article/19/10/1727/1258975), [Criscuolo 2019](https://riojournal.com/article/36178/)). Thanks to the use of the supplementary gamma shape parameter (option `-a`), F81/EI gamma distance allows approximating evolutionary distances derived from complex nucleotide substitution models (the default parameter _a_ = 1.5 enables pairwise distances to be conveniently estimated in many cases).
