HIV-1 Transmitted Founder virus or ancestral strain reconstruction

[Frank Kato]

I have used Single genome amplification (SGA) to generate near full length HIV-1 genomes from key populations in East Africa. I will use part of this data for my MSc Bioinformatics project at Makerere University. But I have challenges in identifying the Transmitted founder virus from this data. 

 

Step used: Plasma > RNA extraction > cDNA preparation > endpoint dilution > HIV half (5' and 3' ) genome Single genome amplification > At least 16 SGA amplicons for each sample Sequenced using Sanger > raw data edited with Sequencher > fasta files exported > the next step is to identify the T/F from these fasta files, but I do not have any idea.  I went on to analyze the multiple sequence fasta output using iqtree -s barcode.fasta -m MFP -asr  in iqtree but I have failed to interpret the data.

[Minh Bui]

Hi there,

What do you mean with “I have failed to interpret the data”?

That does not sound anything to do with IQ-TREE. Or do you mean “IQ-TREE failed”? In that case, please paste the error message from the log here.

Cheers

Minh

On 2 Sep 2021, at 10:19 pm, Frank Kato <sekuw...@gmail.com> wrote:

I have used Single genome amplification (SGA) to generate near full length HIV-1 genomes from key populations in East Africa. I will use part of this data for my MSc Bioinformatics project at Makerere University. But I have challenges in identifying the Transmitted founder virus from this data. 

 

Step used: Plasma > RNA extraction > cDNA preparation > endpoint dilution > HIV half (5' and 3' ) genome Single genome amplification > At least 16 SGA amplicons for each sample Sequenced using Sanger > raw data edited with Sequencher > fasta files exported > the next step is to identify the T/F from these fasta files, but I do not have any idea.  I went on to analyze the multiple sequence fasta output using iqtree -s barcode.fasta -m MFP -asr  in iqtree but I have failed to interpret the data.

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[Minh Bui]

Hi Frank,

After reading your email 2nd time, I think I now understand that “you failed to interpret the output file for ancestral sequence reconstruction”. 

However, I thought this .state file is quite self-readable from the header. See also this doc: http://www.iqtree.org/doc/Command-Reference#ancestral-sequence-reconstruction

You will need a tree viewer to display the node names, to connect this with the information from state file.

Cheers

Minh

To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/1F2232E0-118D-4262-AA4C-5B42FA5D80C8%40univie.ac.at.