# QIIME 1 tree building versus Qiime2 tree building

**URL:** https://forum.qiime2.org/t/qiime-1-tree-building-versus-qiime2-tree-building/9831
**Category:** User Support
**Tags:** phylogeny
**Created:** [May 17, 2019, 10:32pm UTC](https://forum.qiime2.org/t/qiime-1-tree-building-versus-qiime2-tree-building/9831 "2019-05-17T22:32:41Z")
**Posts on this page:** 1
**Showing post:** 1

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### Author: ![TKOneal](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/a9a28c/32.png) [@TKOneal](https://forum.qiime2.org/u/TKOneal)
#### Post date: [May 17, 2019, 10:32pm UTC](https://forum.qiime2.org/t/qiime-1-tree-building-versus-qiime2-tree-building/9831/1 "2019-05-17T22:32:41Z")

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Hi all  
I've been trying to work out a smooth method to analyze a large data set of sequences. In short, it contains 30 samples with 389,340 features and a total frequency of 2,877,374.

I expect this data set to take a while to run through the QIIME 2 workflow, especially in processes necessary to generate the tree but another person was able to run the data through QIIME 1 within a day. Looking at the mask step alone, I've had it running 4 days through command line.  
qiime alignment mafft   
--i-sequences rep-seqs.qza   
--o-alignment aligned-rep-seqs.qza   
--output-dir alignment   
--p-n-threads 0   
--p-parttree   
--verbose

qiime alignment mask   
--i-alignment aligned-rep-seqs.qza   
--o-masked-alignment alignment/masked-aligned-rep-seqs.qza

qiime phylogeny fasttree   
--i-alignment alignment/masked-aligned-rep-seqs.qza   
--o-tree alignment/unrooted-tree.qza   
--n-p-threads 0

I've also attempted to use qiime fragment-insertion sepp  
using default parameters to no avail.

Can anyone suggest what I might be doing incorrect in comparison to their QIIME 1 run?

Thank you for any suggestions or comments.

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