## Orthologs.Phylogenetics.IQTreeCommandline


Command line wrapper for GUIDANCE2.


Usage

``` python
Orthologs.Phylogenetics.IQTreeCommandline(
    cmd="iqtree",
    **kwargs,
)
```


http://guidance.tau.ac.il/ver2/


\>\>\> from Bio.Align.Applications import IQTreeCommandline

You would typically run the command line with clustalomega_cline() or via the Python subprocess module, as described in the Biopython tutorial.


    To maintain IQ-TREE, support users and secure fundings, it is important
    for us that you cite the following papers, whenever the corresponding
    features were applied for your analysis.

    Example 1: We obtained branch supports with the ultrafast bootstrap (Minh et al., 2013) implemented in the
                IQ-TREE software (Nguyen et al., 2015).
    Example 2: We inferred the maximum-likelihood tree using the edge-linked partition model in
                IQ-TREE (Chernomor et al., 2016; Nguyen et al., 2015).
    ################################################################################################################
    # If you used ModelFinder please cite:
        S. Kalyaanamoorthy, B.Q. Minh, T.K.F. Wong, A. von Haeseler, and L.S. Jermiin (2017) ModelFinder: Fast Model
        Selection for Accurate Phylogenetic Estimates, Nature Methods, 14:587-589.

    # If you performed tree reconstruction please cite:
        L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic
        algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 32:268-274. DOI: 10.1093/molbev/msu300

    # If you used partition models e.g., for phylogenomic analysis please cite:
        O. Chernomor, A. von Haeseler, and B.Q. Minh (2016) Terrace aware data structure for phylogenomic inference
        from supermatrices. Syst. Biol., 65:997-1008. DOI: 10.1093/sysbio/syw037

    # If you performed the ultrafast bootstrap (UFBoot) please cite:
        B.Q. Minh, M.A.T. Nguyen, and A. von Haeseler (2013) Ultrafast approximation for phylogenetic bootstrap.
        Mol. Biol. Evol., 30:1188-1195. DOI: 10.1093/molbev/mst024

    # If you used the polymorphism-aware models please cite:
        D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, and C. Kosiol (2016) Reversible polymorphism-aware phylogenetic
        models and their application to tree inference. J. Theor. Biol., 407:362-370. DOI: 10.1016/j.jtbi.2016.07.042

    # If you used the IQ-TREE web server please cite:
        J. Trifinopoulos, L.-T. Nguyen, A. von Haeseler, and B.Q. Minh (2016) W-IQ-TREE: a fast online phylogenetic tool
        for maximum likelihood analysis. Nucleic Acids Res., 44 (W1):W232-W235. DOI: 10.1093/nar/gkw256