qiime2 / q2-phylogeny / 213

100%

push

travis-ci

ENH: Enhancements for IQ-TREE methods within q2-phylogeny. (#58)

Since the last QIIME 2 (2018.8) release [IQ-TREE](http://www.iqtree.org/) has been updated with some relevant features for QIIME 2 users. This [q2-phylogeny PR](https://github.com/mikerobeson/q2-phylogeny/tree/iqtree_enhancements) adds access to several of these new features, as well as some already existing ones.

The following parameters were added to both the `iqtree` and `iqtree-ultrafast-bootstrap` methods:

1) User can perform multiple independent runs for better tree search via `-n_runs`.

> ...10 independent runs outperformed single run in terms of likelihood maximisation.

2) Access to the following [single branch testing methods](http://www.iqtree.org/doc/Tutorial#assessing-branch-supports-with-single-branch-tests) has been added. These quick tests can be used as an alternative, or in conjunction with, traditional bootstrapping approaches. These are: 
    - `-alrt` : SH-aLRT 
    - `-abayes` : aBayes
    - `-lbp` : local bootstrap test

    The user can implement all of the single branch tests concurrently and alongside bootstrapping. 
    The values for each of these are accessible and viewable via [iTOL](https://itol.embl.de/). 

To the `iqtree` method, access to the `-fast` option was added. This option allows IQ-TREE to perform a fast search that resembles FastTree. *This option is not compatible with the ultrafast bootstrap approach.* 

**To the `iqtree-ultrafast-bootstrap` method, the `-bnni` option was added.** From the IQ-TREE docs:
> This option helps to optimize UFBoot trees by NNI on bootstrap alignment. This option reduces the risk of overestimating branch supports with UFBoot due to severe model violations.

Also, the UFboot algorithm has been [updated](https://doi.org/10.1093/molbev/msx281), and its citation added to `iqtree-ultrafast-bootstrap`.

83 of 83 branches covered (100.0%)

213 of 213 relevant lines covered (100.0%)

1.0 hits per line