# Phylogenetic Tree File
**URL:** https://forum.mothur.org/t/phylogenetic-tree-file/21883
**Category:** Uncategorized
**Created:** [July 18, 2023, 6:17pm UTC](https://forum.mothur.org/t/phylogenetic-tree-file/21883 "2023-07-18T18:17:30Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@manuelamiguel](https://forum.mothur.org/u/manuelamiguel)
#### Post date: [July 18, 2023, 6:17pm UTC](https://forum.mothur.org/t/phylogenetic-tree-file/21883/1 "2023-07-18T18:17:30Z")
Hi,
I am having problems to get the phylogenetic tree at the end of my script.
Even asking in my batch file (MCC) a memory of 500 GB and 128 processors, I am not able to get this file (Mothur crashes). Is there any command to manage this issue?
This is the current command:
mothur \> dist.seqs(fasta=final.fasta, output=lt)
mothur \> clearcut(phylip=final.phylip.dist)
Thank you!
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [July 25, 2023, 6:59pm UTC](https://forum.mothur.org/t/phylogenetic-tree-file/21883/2 "2023-07-25T18:59:08Z")
How big is `final.phylip.dist`? How many sequences are in `final.fasta`?
The reality is that modern datasets have so many sequences that it is hard to get a reasonably sized distance matrix that you can use to build a tree. We use a number of “tricks” to get clustering to work that we can’t do with phylogenetic methods. FWIW, I have yet to run into a case where inferences drawn from Bray-Curtis distances are meaningfully different those using weighted UniFrac. That being said, if your reads don’t fully overlap you might need to see this…
> **[Why do I have such a large distance matrix](https://mothur.org/blog/2014/Why-such-a-large-distance-matrix/)**
>
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