# qiime phylogeny
**URL:** https://forum.qiime2.org/t/qiime-phylogeny/22597
**Category:** General Discussion
**Tags:** phylogeny
**Created:** [March 28, 2022, 11:26am UTC](https://forum.qiime2.org/t/qiime-phylogeny/22597 "2022-03-28T11:26:13Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@No.77](https://forum.qiime2.org/u/No.77)
#### Post date: [March 28, 2022, 11:26am UTC](https://forum.qiime2.org/t/qiime-phylogeny/22597/1 "2022-03-28T11:26:13Z")
Excuse me, I would like to ask what is the difference between the iqtree,fatstree and ramxl when using "phylogeny" to build a phylogenetic tree?
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### Author:  [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [March 28, 2022, 2:30pm UTC](https://forum.qiime2.org/t/qiime-phylogeny/22597/2 "2022-03-28T14:30:55Z")
Hi @No.77,
That is a very tricky question to answer as each tool runs slightly different algorithms to generate a tree. You can read more about these tools in our [Phylogeny documentation](https://docs.qiime2.org/2022.2/tutorials/phylogeny/). There is also an associated [Phylogenetic Reconstruction video](https://www.youtube.com/watch?v=0nEabGxFxlY&list=PLbVDKwGpb3XmkQmoBy1wh3QfWlWdn_pTT) which walks through some of this. In a nutshell, each tool uses different types of tree searching algorithms. Some can be better than others given the conditions
My personal take on this... you need to decide between speed vs a thorough tree search / "robust" phylogeny. FastTree2 is made for very large data sets (_e.g._ ~ million sequences), and can run very fast on small to moderate data sets at the potential cost of poor tree generation. While RAxML and IQ-TREE 2, are for smaller data sets and are often considered more thorough (again, your mileage may vary). I highly suggest reading this paper by [Zhou _et al_. 2017](http://dx.doi.org/10.1093/molbev/msx302). There are many papers like this on the subject.
I personally prefer to use IQ-TREE 2 as it will run a model testing algorithm across a few hundred models (this is the default setting in the QIIME 2 phylogeny plugin). After the best fitting model, for your data is selected, IQ-TREE 2 will construct your phylogeny. It can take _a long time_ at this step. But I prefer to generate more accurate phylogenies than making them quickly. Make sure you perform good [quality-control](https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/030-tutorial-downstream/010-filtering.html) and [taxonomic](https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/030-tutorial-downstream/020-taxonomy.html#) filtering prior to tree reconstruction.
Keep in mind, aside from these _de novo_ approaches, there is also a reference-based approach called [fragment insertion](https://library.qiime2.org/plugins/q2-fragment-insertion/16/), which is also included with :qiime2:.
I highly recommend visualizing your tree using [empress](https://library.qiime2.org/plugins/empress/32/). I think a tutorial video for this will appear on our YouTube channel soon.
Sorry I do not have an easy answer for you.
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 28, 2022, 8:30pm UTC](https://forum.qiime2.org/t/qiime-phylogeny/22597/3 "2022-04-28T20:30:58Z")
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