How to convert a FASTA file to an Arlequin file
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- Опубліковано 11 жов 2024
- This tutorial shows you how to make a file for use with the population genetic software Arlequin when starting with a file of DNA sequence data in FASTA format.
This tutorial assumes you are using Ubuntu Linux version 20.04 as your operating system. If you do not have a computer running Ubuntu, fear not. You can install Ubuntu as a virtual machine within your current operating system. It is all free.
The instructions for Windows computers are here:
• Install Ubuntu on Virt...
The instructions for Mac computers are here (from 0:00 to 5:37):
• How to Install Windows...
This tutorial utilizes RStudio:
rstudio.com/
(Rstudio also requires R: www.r-project....)
But you can just use my pre-configured Ubuntu Linux virtual machine! Read more below.
Also, FYI:
I have made a Linux virtual machine that is pre-configured with population genetics and ecological niche modeling programs. I have made videos explaining how to hook up this virtual machine within your Mac or Windows computer, so that you can start using the pre-configured software without having to install any of them (and even without having to install Ubuntu Linux!).
Windows: • Ubuntu 20.04 virtual m...
Mac: • Ubuntu 20.04 virtual m...
Thank you for all this amazing and useful videos! You are saving my dissertation!
These tutorials are a godsend. Thank you, thank you, THANK YOU Josh Banta!!!
This is some incredible work. Thank you for sharing!
Thanks a lot! Such good didactics! You are an excellent teacher!
Best regards from Brazil
Thank you for sharing the information Sir.
hello sir i hope your doing great ...i get the following while converting my fasta to arlequin .......
Error in dimnames(x)
Hey Josh, you are doing great job. I am from Nigeria, without your videos and help, I'd never finish my PhD, at least, not any time soon. Please I have a quick question: I am studying mtDNA, am I going to use diploid or haploid r script? I used haploid knowing that MtDNA is haploid, but the AMOVA, within the group is giving me 100% while among is giving me 0.%. I checked haplotype frequency and I am seeing very few shared haplotype. Please respond. Am I going to select diploid or haploid human mtDNA
Dear Josh, I am trying to run the script for my haploid data, everything is the same, I set the directory and the fasta file has the same name but I have these errors:
Error in dimnames(x)
I have the same error!
My output.arp file was made but it did not read in the sequences. What error could I have made?
Thanks for making such wonderful videos! Please help me. I have a .fasta file but when I load in the R it's reading it as a list while yours as DNAbin. Unable to extract rownames from the list to create outfile. Kindly help. Thanks.
Thank you so much, so helpful!
In the output file groups are not showing can you please give me the solution
Will this work on MSA data? My MSA has gaps in it.
Hi I am wondering why I am getting this error and if this is going to affect the output files?, thanks Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
cannot open file 'output.arp': Permission denied
Hi I solve the issue by shifting to a new directory, thanks
Thank you for your VDO. They are easy to follow. Unfortunately, I cannot download the zip file because it shows only one file. Did I do something wrong?
Dear Apinya, I believe you downloaded the file from the wrong tutorial. I have several different Arlequin tutorials. Click here for the proper one: sites.google.com/site/thebantalab/tutorials#h.39zz6drphh3u
@@DrJBanta Oh yes, I got it, Thank you so much.
Hello sir.... Can I use DnaSP6 to turn the fasta file into an arlequin file?
Hello, I believe you can, sort of, but my experience is that other tools do a terrible job at it. To do it right, I suggest using my tutorial. Best wishes, Josh
than you man!
Didnt work for me. The second run of the R script didnt put any sequence data into the output.arp file.
Dear Melissa, check that you set the working directory to the exact location of your files. Also check that the names of your files in the script exactly match the names of the files you are working with. No spaces or other punctuation can be different. Must match exactly. Good luck - Josh
Hi @@DrJBanta, thank you very much for this useful tutorial! Unfortunately I have the same problem: the names and the working directories are ok. I'm working on Windows... I cannot understand where the problem is!
@@francescalioce7554 Dear Francesca, are you using my tutorial files when you try to run it, or your own data? Best wishes, Josh
@@DrJBanta I am using my files, but in dat
@@francescalioce7554 Dear Francesca, can you send me the files? youtube@joshbanta.com is my email address. FYI, I will be doing a livestream on Tuesday, July 5th where I can go over this problem in more detail. See this link for more details: ua-cam.com/video/z3kpTg-teS4/v-deo.html You can participate in the live stream to ask me questions about it in real time, or you can watch the recorded live stream afterwards.
The R file is not the same on the download page.
Dear Aaron, thank you for alerting me. I have fixed the link. Best, Josh
@@DrJBanta Thank you! Your videos have helped alot!! :)