46
votes
Accepted
Why does the FASTA sequence for coronavirus look like DNA, not RNA?
That is the correct sequence for 2019-nCov. Coronavirus is of course an RNA virus and in fact, to my knowledge, every RNA virus in Genbank is present as cDNA (AGCT, i.e. thydmine) and not RNA (AGCU, i....
- 7,062
25
votes
Accepted
Is it possible for coronavirus or SARS to be synthetic?
The scenarios are impossible and would be laughable if they were not so serious. The evidence is in the phylogenetic trees. Its a bit like a crime scene when the forensics team investigate. We've done ...
- 7,062
17
votes
Why does the FASTA sequence for coronavirus look like DNA, not RNA?
Most sequencing experiments, be it Illumina-based next-generation-sequencing or Sanger sequencing uses DNA as template, not RNA. Even if this virus is RNA-based it would be reverse-transcribed prior ...
- 2,706
16
votes
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11
votes
How do I generate a color-coded tanglegram?
I think you can try dendextend, in this manual there is an example of coloring the branches. I don't think it is exactly like your coloring, but with a little tweaking you might get your colorscheme ...
- 3,521
11
votes
Accepted
What is the best method to estimate a phylogenetic tree from a large dataset of >1000 loci and >100 species
This paper claims that FastTree is almost as accurate as RAxML, while being much faster. You just have to be careful, however, that the support values output by FastTree are not bootstrap values, they ...
- 669
11
votes
Accepted
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?
UPDATE: The article has now been withdrawn with the following note:
This paper has been withdrawn by its authors. They intend to revise it
in response to comments received from the research ...
- 3,472
7
votes
How to create Phylogenetic Trees from fasta files in Python or R?
I would not look for a package for this, but instead build a small pipeline calling external tools with something like the following workflow:
Cluster the ~100 sequences with CD-HIT-EST/PSI-CD-HIT or ...
- 3,472
7
votes
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?
Normally "inserts" used in the manuscript are "indels" in protein alignments, short for insertions and deletions.
What I think has happened is a group investigating indels in HIV env noticed indels ...
- 7,062
6
votes
What is the origin of HIV1?
They are both lentiviruses and share a distant common ancestor.
HIV-1 and HIV-2 are descendents from simian immunodeficiency virus (SIV). The following tree shows the relationships very clearly, from ...
- 7,062
5
votes
Accepted
What is the best way to account for GC-content shift while constructing nucleotide-based phylogenetic tree?
There are models that take into account compositional heterogeneity both under the maximum likelihood and Bayesian frameworks. Although the substitution process is not time-reversible, the ...
- 669
5
votes
Accepted
Are phylogenetic tree construction algorithms any different than general clustering algorithms?
The goal of a phylogeny is to estimate the "expected" number of mutations between all taxa in the analysis and their hypothetical common ancestors. A cluster-analysis will only identify the "observed" ...
- 7,062
5
votes
Accepted
Ancestry of the coronavirus 2019-nCov, WuHan city, China
Overview
The central focus of the tree is to highlight the key biological concern of the new coronavirus, 2019-nCov. The key concern is the genetic similarities to SARS epidemic, and relates to the ...
- 7,062
5
votes
Algorithmic investigation of viral proteins for vaccine design
There isn't a vaccine for any coronavirus, and your question is generally about targeted attentuation, which is a complex area.
The basic building blocks for any vaccine development is virological ...
- 7,062
4
votes
How does one construct a cladogram of intraspecies relationships?
Even with inbreeding and other genetic phenomena that might mask actual evolution of these cultivars, any phylogenetic methodology would be capable of determining relationships accurately.
Try ...
- 182
4
votes
Counting letters in phylip alignment columns with Biopython
using something like for col in column(alignment):
I may get the number of columns which have all the same letters (amino acids)
...
- 1,806
4
votes
Accepted
What is a site in a phylogenetic tree?
A site is simply an individual discrete position, normally a single nucleotide (or amino acid). For example, consider a toy alignment:
...
- 3,472
4
votes
Accepted
Calculate the percentage of each unique phylogenetic tree in a BEAST output
I finally managed to do it in R. Here is my code:
...
- 191
4
votes
How to interpret UniProt allele patterns?
These are cytotoxic T-cell HLA alleles. HLA genotyping is very common and easy to do, so Genbank is the repository.
A*11:01 has very high frequency in Aborigine populations here . You can explore the ...
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4
votes
Are phylogenetic tree construction algorithms any different than general clustering algorithms?
A great question, though a little ambiguous. I don't know what "general clustering algorithms" refer to. For biological sequences, building a tree can be thought as a way of clustering. Anyway...
...
- 5,645
4
votes
For phylogenetic tree construction from core-genome which one is preferable: amino-acid based MSA or nucleotide based MSA?
For a species complex nucleotide phylogenies all the way.
The reason is neutral mutation, which is not observed at the amino acid level because these mutations are part of the degenerate code which ...
- 7,062
4
votes
Accepted
PDB file downloading: pymol automation vs. manual
To expand on the comment by marcin:
fetch downloads files in mmCIF format by default (https://pymolwiki.org/index.php/Fetch). Not all PDB entries have PDB format ...
- 901
4
votes
What is 'k' in sequencing?
It is recommended you learn the degenerate nucleotide code. In sequencing it can signify poor quality sequence data, but in primer design it is useful. R (mutation within purines) and Y (mutation ...
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4
votes
Interpretion of my coronavirus 2019-nCov, Wuhan, China BLAST tree?
The evolutionary related group (clade) of betacoronaviruses you have identified share an amino acid homology of 85% and include SARS. I know this from the underlying tree published on BioRxiv of a ...
- 7,062
4
votes
Why does the FASTA sequence for coronavirus look like DNA, not RNA?
If this were [cDNA], the end of the true mRNA sequence would be ...UCUUACUGUUUUUUUUUUUU, or a "poly(U)" tail.
A cDNA sequence, maybe confusingly, refers to the coding strand of the cDNA (despite ...
- 4,745
4
votes
Accepted
Are the conclusions in "The proximal origin of SARS-CoV-2" legit?
In summary, the authors are saying the complete opposite of "human intervention".
While the analyses above suggest that SARS-CoV-2 may bind human ACE2
with high affinity, computational analyses ...
- 7,062
4
votes
Accepted
Plot information stored in dataframe within a tree (ggtree)
You can accomplish this using the ggtree package available on Bioconductor.
First you will need to combine your tree with the data.
...
- 156
4
votes
Accepted
What is the most appropriate way to find the most recent common ancestor between two distantly related species
Because I've now posted several comments, I'll just roll them all up.
For background on the approaches used to identify most recent common ancestors and a high-level look at how animal taxonomy has ...
- 2,547
3
votes
Accepted
Issues installing Dendropy
You should never install python packages as root or with sudo.
You're already using conda, so ...
- 19.3k
3
votes
How to isolate genes from whole genomes for phylogenetic tree analysis?
Extract desired gene sequences using standalone blast
Simply provide a reference database with your desired output.
Set up your command and away you go. You can set the search up with a for loop ...
- 925
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