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Shorten PoMo usages
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bqminh committed Dec 23, 2017
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47 changes: 10 additions & 37 deletions README.md
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Expand Up @@ -25,42 +25,7 @@ The strength of IQ-TREE is the availability of a wide variety of phylogenetic mo
* __Common models__: All [common substitution models](http://www.iqtree.org/doc/Substitution-Models) for DNA, protein, codon, binary and morphological data with [rate heterogeneity among sites](http://www.iqtree.org/doc/Substitution-Models/#rate-heterogeneity-across-sites) and [ascertainment bias correction](http://www.iqtree.org/doc/Substitution-Models/#ascertainment-bias-correction) for e.g. SNP data.
* __[Partition models](http://www.iqtree.org/doc/Complex-Models/#partition-models)__: Allowing individual models for different genomic loci (e.g. genes or codon positions), mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths between partitions.
* __Mixture Models__: [fully customizable mixture models](http://www.iqtree.org/doc/Complex-Models/#mixture-models) and [empirical protein mixture models](http://www.iqtree.org/doc/Substitution-Models/#protein-models) and.

IQ-TREE PoMo
------------

IQ-TREE+PoMo is still under development. Please check out

iqtree --help

Especially, the section titled `POLYMORPHISM AWARE MODELS (PoMo)`.

```
POLYMORPHISM AWARE MODELS (PoMo):
PoMo is run when
- a Counts File is used as input file, and/or when
- it is specified in the model string (see below).
-st C[FR] or C[FR]ps Counts File (automatically detected).
Useful to customize the virtual population size `ps`
3 <= ps <= 19; ps has to be an odd number, 2 or 10.
F: Sum over partial likelihoods at the tip of the tree (weighted).
R: Random binomial sampling of PoMo states from data (sampled).
Default is `CF9`.
-m <sm>+<pm>+<ft> Default: `HKY+rP+FO`.
<sm>: Substitution model.
DNA: HKY (default), JC, F81, K2P, K3P, K81uf, TN/TrN, TNef,
TIM, TIMef, TVM, TVMef, SYM, GTR, or a 6-digit model
specification (e.g., 010010 = HKY).
<pm>: PoMo model.
- rP (default; reversible PoMo with tree inference).
<ft>: Frequency type (optional; default: +F, counted).
F or +FO or +FU or +FQ.
Counted, optimized, user-defined, equal state frequency.
This overwrites the specifications of the DNA model.
The default model string is: -m HKY+rP+F.
Until now, only DNA models work with PoMo.
Model testing and rate heterogeneity do not work with PoMo yet.
```
* __Polymorphism-aware models (PoMo)__: <http://www.iqtree.org/doc/Polymorphism-Aware-Models>


IQ-TREE web service
Expand Down Expand Up @@ -95,9 +60,17 @@ For the ultrafast bootstrap (UFBoot) please cite:

* D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, and L.S. Vinh (2017) UFBoot2: Improving the ultrafast bootstrap approximation. *Mol. Biol. Evol.*, in press. <https://doi.org/10.1093/molbev/msx281>

When using posterior mean site frequency model (PMSF) please cite:

* H.C. Wang, B.Q. Minh, S. Susko, A.J. Roger (in press) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. *Syst. Biol.* <https://doi.org/10.1093/sysbio/syx068>

When using partition models please cite:

O. Chernomor, A. von Haeseler, B.Q. Minh (2016) Terrace aware data structure for phylogenomic inference from supermatrices. *Syst. Biol.*, 65:997-1008. <https://doi.org/10.1093/sysbio/syw037>
* O. Chernomor, A. von Haeseler, B.Q. Minh (2016) Terrace aware data structure for phylogenomic inference from supermatrices. *Syst. Biol.*, 65:997-1008. <https://doi.org/10.1093/sysbio/syw037>

When using polymorphism-aware models please cite:

* D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, C. Kosiol (2016) Reversible polymorphism-aware phylogenetic models and their application to tree inference. *J. Theor. Biol.*, 407:362-370. <https://doi.org/10.1016/j.jtbi.2016.07.042>

#### Credits and Acknowledgements

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43 changes: 6 additions & 37 deletions utils/tools.cpp
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Expand Up @@ -3719,45 +3719,14 @@ void usage_iqtree(char* argv[], bool full_command) {
<< " Meyer & von Haeseler (2003) method" << endl

<< endl << "POLYMORPHISM AWARE MODELS (PoMo):" << endl
<< "PoMo uses counts files (please refer to the manual)." << endl
<< " -m <sm>+P <sm>: Substitution model." << endl
<< " Only DNA substitution models can be used at the moment." << endl
<< " DNA: HKY, JC, F81, K2P, K3P, K81uf, TN/TrN, TNef," << endl
<< " TIM, TIMef, TVM, TVMef, SYM, GTR, or a 6-digit model" << endl
<< " specification (e.g., 010010 = HKY)." << endl
<< " +P: Use PoMo." << endl
<< " +P{HET}: Optional; fix the heterozygosity to HET (also" << endl
<< " called Watterson's theta or 4*N*mu)." << endl
<< " +P{EMP}: Optional; fix heterozygosity to empirical value from data." << endl
<< "Optional modifiers (affect whole run and not only, e.g., a mixture model component)."<< endl
<< " +N<ps> Set virtual population size N to `ps` (default: +N9)." << endl
<< " 3 <= N <= 19; N has to be an odd number, 2 or 10." << endl
<< " -s <counts_file> Input counts file (see manual)" << endl
<< " -m <MODEL>+P DNA substitution model (see above) used with PoMo" << endl
<< " +N<POPSIZE> Virtual population size (default: 9)" << endl
// TODO DS: Maybe change default to +WH.
<< " +[WB|WH|S] Specify sampling method (default: +WB)." << endl
<< " WB: Weighted binomial sampling method (partial likelihoods at"<< endl
<< " the leaves are set to the probabilities of leading to the" << endl
<< " observed data when sampling WITH replacement)." << endl
<< " WH: Weighted hypergeometric sampling method (partial likelihoods at"<< endl
<< " the leaves are set to the probabilities of leading to the" << endl
<< " observed data when sampling WITHOUT replacement)." << endl
<< " S: Sampled sampling method (determine PoMo states by randomly"<< endl
<< " drawing N bases per site from the data)." << endl
<< " +<ft> State frequency type (default: +F)." << endl
<< " +F or +FO or +FU or +FQ." << endl
<< " Counted, optimized, user-defined, equal state frequency." << endl
<< " This overwrites the specifications of the DNA model." << endl
<< " +G[n] Discrete Gamma model with n categories (default n=4)." << endl
<< " Other types of rate heterogeneity are not yet supported." << endl
<< " +[WB|WH|S] Sampling method (default: +WB), WB: Weighted binomial," << endl
<< " WH: Weighted hypergeometric S: Sampled sampling" << endl
<< " +G[n] Discrete Gamma rate model with n categories (default n=4)" << endl
// TODO DS: Maybe change default to +WH.
<< " The default model modifiers are: `+N9+WB+F." << endl
<< " Model string examples (please refer to the manual):" << endl
<< " -m GTR+P+N15+S" << endl
<< " -m \"MIX{JC+P,HKY+P}+N11\"" << endl
<< " -m \"MIX{JC+P,HKY+P}+FQ\"" << endl
<< " -m \"MIX{JC+P{0.0025},HKY+P}+N13+WB+FO+G4\"" << endl
<< " Example of a standard run:" << endl
<< " iqtree -m HKY+P -s counts_file.cf" << endl
<< " PoMo does not yet support model testing and Model Finder." << endl

<< endl << "ASCERTAINMENT BIAS CORRECTION:" << endl
<< " -m modelname+ASC Correction for absence of invariant sites in alignment" << endl
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