# Parameters in phylogenetic tree creation **URL:** https://forum.qiime2.org/t/parameters-in-phylogenetic-tree-creation/2998 **Category:** User Support **Tags:** mafft **Created:** [February 13, 2018, 4:50am UTC](https://forum.qiime2.org/t/parameters-in-phylogenetic-tree-creation/2998 "2018-02-13T04:50:20Z") **Posts on this page:** 1 **Showing post:** 3
### Author: ![gregcaporaso](https://forum.qiime2.org/user_avatar/forum.qiime2.org/gregcaporaso/32/17769_2.png) [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso) #### Post date: [February 13, 2018, 6:36pm UTC](https://forum.qiime2.org/t/parameters-in-phylogenetic-tree-creation/2998/3 "2018-02-13T18:36:30Z")
Hi @Matilda_H-D, The default parameters used for the `alignment mask` method were derived to match the "Lanemask", which was used in QIIME 1 after running PyNAST (as well as other tools) for filtering very high entropy positions from the alignment before phylogenetic reconstruction. That was a static filter that was specific to one 16S alignment, so we derived these parameters to not be bound to using that alignment. The approach that we take in the _Moving Pictures_ tutorial is known to be a crude approach for developing this tree. We're working on some approaches that are likely to be better, but we started here in QIIME 2 because this approach is not reference-based, and thus doesn't require that we have a reference alignment or tree to work with. You might also be interested in trying out the [q2-fragment-insertion plugin](https://forum.qiime2.org/t/q2-fragment-insertion-community-plugin/1967), which is currently available as a _Community Plugin_ (i.e., one that install independently of the QIIME 2 core distribution). At some point we'll likely transition to using this approach for phylogenetic reconstruction in cases where there is a reference tree available (as is the case for 16S). We will also likely add support for structure-based alignment of 16S using ssu-align to the `alignment` package at some point. Hope this helps! --- _[View the full topic](https://forum.qiime2.org/t/parameters-in-phylogenetic-tree-creation/2998)._