Questions tagged [phylogeny]

Phylogeny is a statistical approach for reconstructing evolutionary relationships using trees

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1answer
459 views

Interpretion of my coronavirus 2019-nCov, Wuhan, China BLAST tree?

This is the BLAST tree of the latest coronavirus out of China (from Wuhan Institute of Virology, China). It seems strange that there is so much divergence from all the other coronaviruses. Is this ...
4
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2answers
3k views

How to convert a phylogeny to a dendrogram in R

I want to convert my phylogeny into a dendrogram so I can use it with dendextend in R to produce a tanglegram. I have made some progress but I keep encountering errors, see below: ...
2
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5answers
102 views

Duplicated genes and genome fragmentation [closed]

This is a follow up question to this post: How can I find out if my gene of interest is duplicated? Briefly, to identify homologous genes, I performed tBLASTn analyses against my genome of interest ...
1
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2answers
391 views

How to define an outgroup to build a robust amino acid tree

I building a robust amino acid phylogeny with adequate robustness support (see previous post here). This is a brief summary of what I have done: I performed a BLASTp analysis using a protein sequence ...
1
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1answer
89 views

How to make a robust amino acid phylogeny with adequate robustness support

This is the second part of this thread: Duplicated genes and genome fragmentation As @Michael G. suggested, I did a pseudo-annotation of sequences 5-2 and 5-3 (i.e., I joined both sequences into one)...
0
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1answer
67 views

Minimal working example for phylogenetic tree construction in R using an alignment of DNA strings and a vector of names?

I am looking at how to build a phylogenetic tree in R from aligned genetic information (dna sequences). There are multiple ...
19
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1answer
2k views

Is it possible for coronavirus or SARS to be synthetic?

I have heard several conspiracy theories regarding the origin of the new coronavirus, 2019-nCov. For example that the virus and/or SARS were produced in a laboratory or were some variant of Middle ...
3
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2answers
176 views

How to find/build the evolutionary history of a protein from its sequence?

I'd like to build the evolutionary history of a protein, given its sequence. Namely, given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein as an example: ...
10
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3answers
2k views

A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean?

Quote: We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have ...
5
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1answer
848 views

Ancestry of the coronavirus 2019-nCov, WuHan city, China

In one of the answers to another question about the corona virus a link was given to this phylogenetic analysis of the virus. Can somebody assist a non-bio type here? It seems to show that the ...
1
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1answer
56 views

How to allow "half windows" in biopython?

I am using Biopython to examine protein sequences including the Kyte and Doolittle hydrophobicity. However, for short sequences, this returns an empty value; the value is not allowed if the window ...
1
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2answers
440 views

How can I find out if my gene of interest is duplicated?

To identify homologous genes, I performed tBLASTn analyses against my genome of interest resulting in sequences of a closely related species. Using this method, I found two (and in some cases up to ...
1
vote
1answer
104 views

What does instantaneous rate matrix mean?

PhyML is a tool used for maximum likelihood estimation analysis. I was running a PhyML analysis to check the rate of nucleotide change in DNA sequences and in the PhyML output, there are rate ...
1
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2answers
4k views

How to show bootstrap values on a phylogenetic tree constructed with RAxML

I apologize for this very basic question. With @Michael G.'s help, I have been learning how to use RAxML to build a phylogenetic tree (How to define an outgroup to build a robust amino acid tree) and ...
1
vote
1answer
145 views

Interpreting quantitive outputs from maximum likelihood phylogenetic trees

I ran a calculation in RAxML to determine the majority consensus phylogeny of a maximum likelihood bootstrap (How to show bootstrap values on a phylogenetic tree constructed with RAxML), and I got ...