Questions tagged [phylogenetics]

Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.

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Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

The SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it... ...
Rebecca J. Stones's user avatar
34 votes
4 answers
9k views

Why does the FASTA sequence for coronavirus look like DNA, not RNA?

I'm looking at a genome sequence for 2019-nCoV on NCBI. The FASTA sequence looks like this: ...
jameshfisher's user avatar
12 votes
5 answers
341 views

Improve a reference genome with sequencing data

I have a DNA sample which I know doesn't quite match my reference genome - my culture comes from a subpopulation which has undergone significant mutation since the reference was created. The example I ...
Scott Gigante's user avatar
4 votes
2 answers
4k 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: ...
AudileF's user avatar
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4 votes
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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 ...
Loopy's user avatar
  • 41
2 votes
5 answers
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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 ...
Leah's user avatar
  • 113
1 vote
2 answers
676 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 ...
Leah's user avatar
  • 113
1 vote
2 answers
53 views

Improving list speed: glycosylation example

I discussed a question with @gaspanic Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions . The issue emerged was speeding up lists in Python. ...
M__'s user avatar
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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)...
Leah's user avatar
  • 113
0 votes
1 answer
109 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 ...
Vass's user avatar
  • 178
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1 answer
1k views

Using Entrez.efetch() to retrive .fasta file from any NCBI database?

I tried to use these python codes to retrieve a .fasta file from gene database, but the output were the parameters of the report ...
DurianDan's user avatar
19 votes
1 answer
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 ...
Sscheme's user avatar
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9 votes
3 answers
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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 ...
SurpriseDog's user avatar
6 votes
2 answers
415 views

Theoretical limit of human genome compression

How small can a compressed file containing the human genome be? I'm aware that this question cannot actually be answered, since it is asking for the Kolmogorov complexity of the human genome, which is ...
Rexcirus's user avatar
  • 171
5 votes
3 answers
4k views

How to translate amino acid sequences to Nucleotide sequences

I want to convert a list of fasta ( protein sequences) in a .text file into corresponding nucleotide sequences. A Google search gives me result of DNA to protein conversion but not vice versa. Also, I ...
user3289492's user avatar
5 votes
1 answer
891 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 ...
puppetsock's user avatar
4 votes
1 answer
414 views

Programmatically retrieve Metadata from SRA Run Selector

I previously asked a question about how to retrieve the Accession List associated with a SRA project. The answer was: ...
An Ignorant Wanderer's user avatar
3 votes
2 answers
244 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: ...
0x90's user avatar
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3 votes
1 answer
2k views

Downloading SRA Files from AWS

I want to download the original BAM files that the authors had uploaded to SRA. Normally, I would just use sam-dump, but the files are having issues that seem ...
merv's user avatar
  • 621
3 votes
4 answers
863 views

Comparing phylogeny in R

So I want to compare the phylogeny created using two methods for example Maximum likelihood and maximum parsimony.Is there any way to compare the two phylogeny ? I did read about phangorn but not ...
kcm's user avatar
  • 1,694
2 votes
1 answer
133 views

Programmatically retrieve Accession List from NCBI

I would like to programmatically retrieve the file "Accession List" from an NCBI page. I'm running firefox, so I'm clicking the file and clicking Ctrl + <...
An Ignorant Wanderer's user avatar
2 votes
4 answers
250 views

How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?

I would like to download a number of SARS-CoV-2 fastas from NCBI/Genbank using a web endpoint. I looked on their website but it's confusing. I have the accession numbers, but can't figure out how to ...
Cornelius Roemer's user avatar
2 votes
2 answers
197 views

What is the file .mums created by mummer?

I am doing genome sequence alignment using MUMmer, in particular I want to do a dotplot with mummerplot. So the passages that I did are: 1.create a file .mums with the following command line: ...
HelpNeederStudent's user avatar
2 votes
1 answer
307 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 ...
Leah's user avatar
  • 113
1 vote
1 answer
50 views

building complex drug-dna for AMBER software

I will appreciate if you can please clarify some of my doubts about drug-DNA complex. I want to study the drug-DNA simulation using AMBER. I did go through all the tutorials video on youtube but ...
dnalectronics's user avatar
1 vote
2 answers
2k views

Generating PDB file for custom DNA sequence

I asked this question in biology.stack exchange and was referred to this community. I am going to request migration for this question. https://biology.stackexchange.com/q/105024/67415 I want a PDB ...
dnalectronics's user avatar
1 vote
2 answers
7k 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 ...
Leah's user avatar
  • 113
1 vote
1 answer
33 views

How to use Gblocks for trimming single-copy gene sequences?

I have run OrthoFinder on a set of 11 genomes and got the results in a folder. From the output folder, I saved all the single-copy gene sequences in a single FASTA file and now wish to remove all gaps ...
Kirti Kulanthaivel's user avatar
1 vote
1 answer
185 views

reverse translation from amino acid string to DNA strings

what is the opposite of .translate() function calls ? I mean let's say I am given an amino acid string CYCLIC, how do I obtain all the possible combinations of DNA ...
kevin's user avatar
  • 143
1 vote
2 answers
94 views

Phylogenetic tree building from proGenomes database for shotgun metagenomics

For some weeks I'm fighting with an issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account phylogenetic distance. I’m ...
MagíBC's user avatar
  • 41
1 vote
2 answers
695 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 ...
Leah's user avatar
  • 11
1 vote
1 answer
58 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 ...
James's user avatar
  • 409
1 vote
2 answers
57 views

Multiple Alignment cost application

Is there any biological application/case where someone would be interest in the estimated total cost of the alignment between a set of sequences (genes or amino acids) without the aligned sequence ...
gcorso's user avatar
  • 149
1 vote
1 answer
248 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 ...
Anthony Guterres's user avatar
1 vote
2 answers
161 views

Compressing the human genome to few megabytes

Multiple sources (see for instance this or this) discuss how genetic data will have scalability problems, given the huge file size of the human genome. The most straightforward encoding (see here) of ...
Rexcirus's user avatar
  • 171
1 vote
2 answers
2k views

Why do NEB adapters have non-complementary sequence?

I am making some infographics of different library prep types and noticed something weird about NEB's Ultra II adapters. Molecule 1 is the desired product of the ...
conchoecia's user avatar
  • 3,111
0 votes
2 answers
405 views

parsimony and maximum likelihood tree comparison in R

Maximum Likelihood analysis compares the tips or the species based on their sequence similarity while Parsimony analysis compares the characteristic features among the species. So far I did ...
kcm's user avatar
  • 1,694
0 votes
1 answer
71 views

Single or partitioned model for supermatrix tree inference?

I am dealing with several genes in my dataset. For each of the genes, I have built gene tree, with their best estimated model. I am intended to look into the effect of the tree from concatenated ...
web's user avatar
  • 11
0 votes
1 answer
123 views

Calculating Synonymous and non-synonymous

library(seqinr) library(ape) library(phangorn) alignment file data file sylvia.aln <- read.alignment("abhi_seq/all_seq_no_gal.fas", format="fasta") ...
kcm's user avatar
  • 1,694
0 votes
2 answers
55 views

How to obtain desired output?

I am working on a project using the following command within nano: ...
andnowmywatchbegins's user avatar