Questions tagged [phylogeny]

Phylogeny is a statistical approach for reconstructing evolutionary relationships using trees

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What exactly is a reasonable evolutionary criterion? [closed]

I got a rejection of publication which the reviewers mainly point out as not following a reasonable evolutionary criterion for choice of species used for phylogeny creation. In our dataset, a list of ...
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1answer
34 views

Simulation of DNA sequences through substitution rates

I'm looking for a little bit of guidance. My question is regarding the simulation of DNA sequences with a fix substitution rate. The majority of the programs for simulating sequences use Continuous ...
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1answer
13 views

Constructing a phylogenetic tree for classical MHC genes from different organisms

I am interested in constructing a phylogenetic tree containing the classical HLA α1 and α2 domains and potential classical MHC α1 and α2 domains of a different organism. I am using the amino acid ...
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21 views

Tool that can sort NCBI taxonomy ids based on phylogeny

I have a set of NCBI txids (of varying ranks) that I want to sort in some way (e.g. a table or a tree, the way it is sorted isn't super important), based on the current NCBI data for phylogenetic ...
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35 views

Does the alignment need to be redone when using SAW method to test long branch attraction?

I am looking into different methods to test the long-branch attraction problem. In this chapter they talk about the SAW method - excluding one and the other taxa from the dataset and see if they ...
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1answer
23 views

calculating phylogenetic tree from pairwise distances

I have a file with a 3-column list of pairwise distances: A B distance A C distance B C distance ... And I would like to calculate a phylogenetic tree for all the ...
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1answer
51 views

Can't load files into PopART

I am trying to create haplotype networks in PopART which I have successfully done many times in the past. 2 weeks ago the program was working fine for me but recently I am unable to load files. What ...
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12 views

How to decide whether to assume 2 Gene Losses or 1 to find minimum cost trees for Gene Duplication/Expression events?

This paper introduces an approach to estimate a convergence from discord between phylogenetic species trees and gene trees, using Gene Duplication and Expression events. A Gene Duplication (GD) event ...
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Computing Maximum Agreement Subtree of two unrooted phylogenetic trees with PhyloNet?

I am using PhyloNet to compute the MAST of two unrooted binary phylogenetic trees but I am not getting the output that I should. I think the issue might be with the way I am writing the trees in the ...
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38 views

Mrbayes stop at certain generation without error

I am using Mrbayes v 3.2.7 MPI version to infer phylogeny, and I set the ngeneration to 10,000,000, but it often stop at certain generation (usually far smaller than given generations). Even if I ...
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1answer
30 views

Build tree to calculate beta diversity

I am trying to calculate beta diversity using the UniFrac distance on my data, each sample having OTUs values. To calculate it, I saw it required building a tree with percentages that represented the ...
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1answer
55 views

How to import a phylogenetic tree (in nexus format) with node support values in R

I have a phylogenetic tree in nexus format that was generated with RAxML. In the tree file, there are node support values. I want to plot this tree in R with the support values showing. However, when ...
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1answer
38 views

Create a NHX phylogeny format with r or python

I need help to add information in my phylogenetic tree on each branch. I have two pieces of information at my disposal: 1 ) A phylogenetic tree in newick format : <...
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1answer
29 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 ...
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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 ...
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2answers
42 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 ...
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1answer
107 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 ...
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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 ...
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1answer
69 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 : ...
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1answer
28 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 ...
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0answers
45 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 ...
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2answers
279 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: ...
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1answer
32 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 ...
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74 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 ...
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1answer
51 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 ...
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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 ...
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1answer
50 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 ...
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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 ...
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1answer
135 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 ...
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1answer
49 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. ...
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1answer
43 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 ...
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1answer
207 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%?
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1answer
34 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 ...
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1answer
41 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 ...
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1answer
40 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 ...
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1answer
48 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 ...
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1answer
56 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 ...
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1answer
548 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 ...
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1answer
135 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 ...
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1answer
84 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 ...
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1answer
98 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 ...
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1answer
119 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 ...
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1answer
31 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!!!
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1answer
60 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 ...
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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 ...
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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 ...
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1answer
102 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 ...
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2answers
77 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 ...
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1answer
41 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 ...
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1answer
86 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 ...