Questions tagged [phylogeny]

Phylogeny is a statistical approach for reconstructing evolutionary relationships using trees

Filter by
Sorted by
Tagged with
0
votes
1answer
8 views

Dataset showing evolution of gene

As a way to exemplify how the hierarchical clustering of particular DNA sequences can be used to derive phylogenetic trees, I'm looking for a (even very small) dataset of the same genes (or other ...
0
votes
0answers
14 views

How to calculate dN/dS for all ortholog group? [closed]

I have managed to generate json file for all ortholog groups (4000) under HyPhy using BUSTED, SLAC and FEL. From the output, how can i find the dN/dS and how shall i compare among all of the groups ? ...
0
votes
0answers
8 views

Can we use reference strain as an out-group strain to root SNP based species tree?

I have generated a species tree based on whole-genome SNP using CSI_SNP_Phylogeny, wherein I used Reference strain as an outgroup to root my species tree (SNP fasta were downloaded and RaxML used to ...
0
votes
1answer
26 views

Consensus on how to select SNPs for creating a phylogeny when the full dataset is too large

I have got a quite large VCF file (about 20k samples with 160k SNPs after filtering for quality etc.) and I would like to get a phylogeny for it. However, the whole dataset's too large for my ...
4
votes
1answer
99 views

What origins for virus HIV1?

What origins for virus HIV1? This is the alignment of a small part of the POL protein of the HIV1 virus GenBank KU749412.1, with the POL protein of the Visna virus GenBank L06906.1 ...
2
votes
0answers
29 views

Analyzing and visualizing metagenomic data

I am starting out in metagenomics, Aim I wish to understand the whole analysis from the raw reads to interpretation. Background My current pipeline is used for: analyzing human gut microbiota cleans ...
2
votes
1answer
38 views

Plot information stored in dataframe within a tree (ggtree)

Hello to the entire Stackoverflow community! I'm writing to you because I'm currently building a phylogeny with ggtree and I have in parallel a table like this one: df : ...
1
vote
1answer
27 views

Measure the purifying selection for certain taxa along a phylogeny

I am posting this message because I need clarity about the analysis I want to perform. In my analysis, I have a homologous gene in 13 species, and I would like to evaluate the selection pressure of ...
1
vote
0answers
38 views

Comparison of phylogeny of SARS2 whole genome vs spike genome

I’ve built two phylogeny at minimum evolution in MEGA-X and extracted these as newick files. My next step is to compare the two phylogeny to look at if the mutations within SARS2 are more prevalent ...
1
vote
2answers
126 views

Download complete Phylogenetic Tree as JSON

I would like to integrate the phylogenetic tree into a website. Does anyone know where I can download the complete tree? Best would be a JSON, which looks something like this: ...
1
vote
1answer
29 views

panic: division of zero by zero or infinity by infinity error when running GODON positive selection analysis

I am using godon to find genes under positive selection with the branch-site test. However, after running for a little while I get the error "panic: division ...
1
vote
0answers
16 views

GCF VS GCA or combination of both for pangenomic studies

I have just started to learn bioinformatics and pangenomics. So if this question seems to you pretty basic then I apologize in advance. As we know, NCBI for the genome database, there are two kinds of ...
1
vote
1answer
47 views

how to estimate phylogeny without DNA sequences?

I am new to bioinformatics, I am reading ‘Analysis of Phylogenetics Second Edition and Evolution with R’ from Emmanuel Paradis. I can create phylogeny from DNA sequences, by first calculating the ...
0
votes
1answer
43 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 ...
2
votes
1answer
43 views

Standard for when to collapse phylogenetically uninformative nodes

I have been creating phylogenetic trees using RAxML (using Boostrap + ML) and I end up with a bestTree file, outputted in newick format. When I open up the tree in FigTree, I notice that it collapses ...
2
votes
1answer
59 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
vote
1answer
69 views

Adding external annotation to the phylogeny tree

I was looking to overlay annotation on my phylogeny made,which was solved here question asked where i was looking to compare two different phylogeny which i could do. Now i want to label the tips ...
1
vote
1answer
42 views

Why does the Genbank phylogenetic tree of 4000 sars-cov-2 sequences only display 200 nodes?

I manually selected all 4000 sequences on the 20 pages of the SARS-CoV-2 sequences on genbank here. When I click on Build phylogenetic tree, it only has 200 nodes. ...
1
vote
1answer
30 views

Generate an approapite output from DNaSP6 to Arlequin program

I am performing a haplotype and nucleotide diversity of my Sanger sequences (from Watermelon mosaic virus coat protein region) by Arlequin program with the aim to see the probability that two randomly ...
1
vote
1answer
101 views

Can I use BioEdit to quantify the sequence similarity?

I am using BioEdit. It can perform an align of multiple sequences. Can this sequence similarity be outputted as a value, e.g. 70%?
2
votes
1answer
32 views

Assemble reads for a specific gene

I have a lot of unassembled sequencing data and I want to build phylogeny for some genes from these data. I can retrieved the sequene by mapping reads to a reference sequence but if the two species ...
1
vote
1answer
37 views

After KEGG and GO analysis, how to make tables+phylogenetic trees

hope everyone is ok. I used Trinity to do a de novo transcriptome assembly, then blastp/blastx and then used Blast2GO software to do KEGG and GO analysis. So i got some txt files with header : for GO ...
0
votes
1answer
36 views

Phylogenetics analysis between diverse species

Hope everyone is well. So i was appointed with a task, and i need some guidance. Attention, the one that gave me the task may not have explained this very clearly. I will write what he exactly asked ...
1
vote
1answer
40 views

Why do we scale the rate matrix of a substitution model to make the average rate of substitution equal 1?

The matrix of transition probabilities for a substitution model Q over time t is found as follows: $e^{Qt}$. Since Q and t only show up as a product, we cannot distinguish time and rate of change. So ...
0
votes
1answer
52 views

Relationship between the instantaneous rate of change of a continuous time Markov model and the rate of a global clock model?

If continuous-time Markov models contain a parameter q that denotes the instantaneous rate of change and a global/strict clock model is the overall rate of evolution, how are these two parameters ...
3
votes
1answer
419 views

Are the conclusions in “The proximal origin of SARS-CoV-2” legit?

I don't have any background in genetics and bioinformatics, so I ask you if you think that the arguments provided in the article The proximal origin of SARS-CoV-2 by Andersen et al. are convincing. In ...
4
votes
1answer
115 views

Comparing phylogenetic models with different datasets

I'm a linguist interested in phylogenetic tree inference using language data. I'm posting here because I'm using Bayesian phylogenetic methods in my work (probably using BEAST and/or RevBayes). For ...
2
votes
1answer
41 views

How to construct the phylogenetic tree of the “High Recombination” genus streptomyces?

I need to construct the phylogenetic tree of the whole genus of streptomyces. And my goal is to find out how my target strep species distributed in the whole strep genus and obtain the distribution ...
3
votes
1answer
95 views

Coronavirus phylogeny and evolution

This new article presents the phylogeny of the coronaviruses and the placement of the new coronavirus in it. This made me wonder of what we know about the coronavirus evolution, particularly where it ...
2
votes
1answer
79 views

How many single copy gene are needed to construct the phylogenetic tree?

I ran the orthomcl program with genomes of the whole streptomyces genus(from ncbi) as input, but I only got 22 orthologous groups(streptomyces's genome size vary from 2M to 15M, which shows the great ...
1
vote
1answer
30 views

How to seperate the genus into different group based on th ANI calculation?

I've calculated the ANI of the streptomyces genus, but I'm confused about how to separate them into a different group, could anybody kindly tell me how to do that? Thanks!!!
1
vote
1answer
43 views

How to construct the phylogenetic tree of the whole genus?

I am confused about how to construct the phylogenetic tree of the streptomyces genus. The taxonomy of the streptomyces genus is mostly based on the MLST method, but now I need to use the gene data ...
-2
votes
1answer
149 views

Algorithmic investigation of viral proteins for vaccine design [closed]

I wish to investigate how a virus could be attenuated through targeted mutagenesis by a priori prediction of attenuating amino acid mutations. In particular, I am seeking bioinformatic solutions where ...
1
vote
2answers
45 views

Download sequences of isoforms

I want to collect all isoforms of all genes (Fasta/Fastq file of nucleotide and protein sequences) Arabidopsis Col-0. I am wondering if there is a straightforward way to download the file from any ...
1
vote
1answer
88 views

a package with randomization/permutation tests for genomic analyses

please would you let me know, is there a package in R/python/C that has implemented randomization/permutation tests for joint genomic analyses (an example of joint genomic analyses -- when jointly ...
0
votes
2answers
64 views

efetch nucleotide -> protein ids

I'm downloading translated viral genomes initially via Blast - which had shortcomings - and now by efetch. What I want to do is obtain a complete list of all ...
3
votes
1answer
31 views

Database with antigens and current vaccines

I am seeking a virological database comprising the following information: vaccine. antibody receptor. Preferably hosting multiple strains/samples of a given virus samples of strain. Any assistance ...
0
votes
1answer
85 views

How can i get data set of illness and not illness people?

I'm reading a virology paper where the authors made a classification for the patients as to whether they had a specific disease outcome or not against the underlying sequence ... The research focused ...
1
vote
2answers
268 views

How to create a .phy file for constructing a phylogenetic tree?

I'm new here. I need to construct a phylogenetic tree from 16s Sequence data (merged 151 bp) and color the branches/nodes based on my experimental conditions. From this blog, it looks like I need a ....
-1
votes
1answer
313 views

How to generate ultrametric phylogenetic trees?

I have generated rooted species tree with 1000 bootstraps by RAxML. Further, I need to generate ultrametric tree for the same. Therefore, Please suggest me how to generate ultrametric tree from the ...
2
votes
2answers
93 views

Detecting whether genome is genetically engineered?

Is there a methodology for detecting whether a genome has been tampered with by a biologist? For instance, say there has been an ebola outbreak such as in "The Andromeda Strain". Is there a way a ...
1
vote
0answers
35 views

Algorithmic Information Measurement of Human Genome Databases?

What is the highest data compression ratio achieved on a population of genomes measured to include the compressing algorithm itself? The size of the compressed database approximates its algorithmic ...
28
votes
5answers
8k 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: ...
16
votes
1answer
1k 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 ...
10
votes
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 ...
4
votes
1answer
443 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 ...
6
votes
2answers
829 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 ...
8
votes
2answers
662 views

What is 'k' in sequencing?

When a DNA sequence is sequenced, I've only ever dealt with A,T,C,G and N which indicates un-identifiable bases. However, I came across a 'k' recently and I had asked another researcher who gave me an ...
1
vote
1answer
95 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 ...
1
vote
1answer
50 views

What software can I use to develop a population haplotype network?

I looking for software to conduct a haplotype network using cytochrome oxidase (CO1) mitochondrial sequence data to study population structure in Anopheles mosquitoes.