von drop et al 2020 Nat Communication, no evidence for increased transmission from recurrent mutations in SAERS-COV-2

The authors proposed a sister clade comparison method to detect transmission changes. The paper claim it is unbiased based on simulation and random permutation.  

in von dorp 2020, D614G has linkage disequilibrium with 3 other SNPs, and claim that no evidence support that D614G is associated with higher transmission. 

Potential caveats include low genetic diversity.  

HQ thinks the author did not address the methological problem of the phylogenetical method of bifurcation. What if it is a phylogenetic network? The author acknowledged that bifurcation and clade often have low support. 

Protocol for using MEGA to generate a 16s rDNA tree for giant panda evolution

Overview:
We will first align the 16s rDNA sequences and then generate a neighor-joining tree.

The steps are illustrated below:

Start MEGA6 software

Click "File" --> "Open A File/Session", Choose "panda_16srDNA.fas". 

 Choose "Align"

Click "Alignment"-->"Align by ClustalW"

Click "OK" to select all sequences, 

Click "OK" to accept the default setting for alignment

Click "No", because 16s rDNA is an RNA coding sequence

Your sequences are now aligned. 

Click "Data" -->"Export Alignment"-->"MEGA Format"

Input an appropriate file name. 

Input an appropriate title: 

Choose "No" because 16s rDNA is not protein-coding gene.

Now, we can start to generate a phylogeny. 

At the main MEGA window, click "Phylogeny" -->"Construct/Test Neighbor-Joining Tree": 

Choose the appropriate alignment file, and then "Open"

Click "Computing" to use the default setting

Generated tree (only partial picture is shown here)

Save your image to use in your lab report.

polytopes and phylogeny

polytopes is the convex hull

http://en.wikipedia.org/wiki/Polytope

tree -> matrix as markov process  OR polytope

Phylogeny lab, west nile virus using envelop glycoprotein squences

Download MEAG from www.megasoftware.net
This menu is written for a Windows computer.  Toolbar features are slightly different in Mac.

Open file "WNV.mas" with MEGA.  (In Mac, you need to start MEGA first, and then look for this file.)

In "Alignment Explorer", click "Translated Protein Sequences"

 Click "Yes" for selection and genetics tables.

 Translated proteins should look like this

Choose "Alignment" by "Align by ClustalW"

"OK" to use the default alignment setting.

Click "Data" -> "Export Alignment" -> "MEGA format".

Input title for the alignment

This alignment are for "protein coding sequences". 

In the main window of MEGA, choose "Phylogeny" -> "Construct/Test Neighbor-Joining Trees"

Choose default parameters.

We should be able to see the generated tree.

In order to save the image, we can "Image"->"Copy to Clipboard".

And then "Paste" to a WORD document. 

Note: Please feel free to explore many other features of MEGA. 

Reference:
Online MEGA help file, http://www.megasoftware.net/webhelp/helpfile.htm