<p>I want to create a phylogenetic tree using a 3.8MB FASTA file with ambiguous code. How can I perform multiple sequence alignment and the construction of phylogenetic tree with these ambiguous codes?</p>
<p>Could you please suggest some programs or R packages to complete this task?</p>
<p>How does MEGA11 software handle ambiguous codes? Will the alignment consider them to be mismatches?</p>

CC BY-SA 4.0
2023-06-08T04:34:00.997Z
Welcome @user17615. Firstly, I would recommend starting with a pilot study and then scale up. What is the genetic distances or taxonomic groups between the sequences, e.g. species, genera, families, orders (thats quite important)? Is it essential to do this in R, or what the requirements for R, e.g. is that the language you work in? Finally, how is your bash/Linux command line?
M__
CC BY-SA 4.0
2023-06-09T04:24:46.700Z
MegaX is poor for this purpose, it handles sequence ambiguities. The file sizes for complete phylogenetic analysis within R is going to be very tough, but its doable using "soft statistical approaches" for phylogenetic methods and can be processed via the `ape` library.
M__
<r><phylogenetics><fasta>
Phylogenetic tree from a large FASTA file
# Phylogenetic tree from a large FASTA file

(Asked by: username_0 on 2023-06-08)

I want to create a phylogenetic tree using a 3.8MB FASTA file with ambiguous code. How can I perform multiple sequence alignment and the construction of phylogenetic tree with these ambiguous codes?

Could you please suggest some programs or R packages to complete this task?

How does MEGA11 software handle ambiguous codes? Will the alignment consider them to be mismatches?

**Tags:** r, phylogenetics, fasta
> **Comments:**
> **username_1**: Welcome @user17615. Firstly, I would recommend starting with a pilot study and then scale up. What is the genetic distances or taxonomic groups between the sequences, e.g. species, genera, families, orders (thats quite important)? Is it essential to do this in R, or what the requirements for R, e.g. is that the language you work in? Finally, how is your bash/Linux command line?  
> **username_1**: MegaX is poor for this purpose, it handles sequence ambiguities. The file sizes for complete phylogenetic analysis within R is going to be very tough, but its doable using "soft statistical approaches" for phylogenetic methods and can be processed via the `ape` library.  

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