# Suggestions to speed up phylogenic tree construction? **URL:** https://forum.qiime2.org/t/suggestions-to-speed-up-phylogenic-tree-construction/29741 **Category:** General Discussion **Created:** [March 29, 2024, 1:44pm UTC](https://forum.qiime2.org/t/suggestions-to-speed-up-phylogenic-tree-construction/29741 "2024-03-29T13:44:29Z") **Posts on this page:** 1 **Showing post:** 11
### Author: ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer) #### Post date: [March 29, 2024, 6:04pm UTC](https://forum.qiime2.org/t/suggestions-to-speed-up-phylogenic-tree-construction/29741/11 "2024-03-29T18:04:37Z")
> [@aabrams](#): > > but most tutorials/forums were saying that it was unnecessary if you were using Dada2 since it performs this function and you only needed to use Cutadapt if barcodes were present.... This is not entirely true, for the reasons I explained. Also, cutadapt is often used to simply remove the primer sequences from the reads. That is, enter in the PCR primer sequence in 5' - 3' direction for the forward and reverse primers. There are many examples in the forum on this specific use case. See the following: > [@Removing Primers: Cutadapt vs Denoising](https://forum.qiime2.org/t/removing-primers-cutadapt-vs-denoising/20376/2): > > Hi @elsamdea These are good questions! You are correct... technically you can go either way... that is use cutadapt, or just trim the primers out directly within deblur or DADA2. I prefer to use cutadapt to remove primers for the following reasons, which I think I've echoed elsewhere in the forum a few times: There may be spurious off-target sequences within your data. Just trimming will retain these reads. PCR / sequencing errors can add or remove bases from the beginning or end. Thus pote… > [@Remove Primer in paired-end demultiplexed file](https://forum.qiime2.org/t/remove-primer-in-paired-end-demultiplexed-file/17376/8): > > Hi @mohsen_ej, if you search the forum, you'll come across many examples of how to use cutadapt. There are quite a variety of ways to leverage this tool. You'll likely just want to specify your specific primer sequences not the entire construct. That is, your primers are likely these (anything after the ...GAGACAG): --p-front-f CCTACGGGNGGCWGCAG \ --p-front-r GACTACHVGGGTATCTAATCC \ Here are a couple to get you started: -Mike --- _[View the full topic](https://forum.qiime2.org/t/suggestions-to-speed-up-phylogenic-tree-construction/29741)._