Questions tagged [phylogenetics]

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

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4answers
138 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 ...
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1answer
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Phylogenetics software that can represent collapsed nodes as triangles

I am trying to represent a large (100-300+ sequences) phylogenetic tree in a way that gets my point across. I figured that reducing the number of branches (by collapsing clades which include highly ...
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1answer
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phangorn fasta file read error

Im trying to read a multifasta sequence file into phangorn I get the following error ...
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1answer
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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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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
36 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
41 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
99 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
31 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
77 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
63 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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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
36 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
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Algorithmic investigation of viral proteins for vaccine design [closed]

I wish to investigate how a virus could be attenuated through targeted mutagenesis by investigating its protein mutations in order to produce an efficacious vaccine. Are there examples where the ...
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2answers
43 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
74 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
52 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
29 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
45 views

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

I'm new to bioinformatic .. i'm reading a paper and what i got that they made a classification for the people if they have a sequence of a disease or not ... ...
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2answers
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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 ....
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1answer
93 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 ...
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1answer
75 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 ...
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3answers
101 views

Edit all the fasta headers using awk

kindly your comment highly appreciated have more than 4k header sequences look like: ...
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0answers
33 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 ...
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5answers
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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: ...
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1answer
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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 ...
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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 ...
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1answer
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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. It seems strange that there is so much divergence from all the other coronaviruses. Is this expected of new diseases?
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2answers
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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 ...
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2answers
423 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 ...
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1answer
57 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 ...
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1answer
29 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.
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1answer
89 views

which NCBI tool is optimized to identify a species from a DNA fragment?

“The Iceman” was a man who lived 5300 years ago and whose body was recovered from an Alpine glacier in 1991. Some fungal material was recovered from his clothing and sequenced. Ice man : found as a ...
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1answer
47 views

How to extract hypervariable region of mitochondrial dna from its fasta file?

Recently I've done some analysis on human mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed ...
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2answers
629 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 ...
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0answers
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Calculating the trimming parameter when constructing an additive phylogeny

How do you calculate the trimming parameter when constructing an additive phylogeny? I think it has a relationship with the the length of the shortest hanging edge but I can not figure out how this ...
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4answers
118 views

tool to visualize a collection of phylogenetic trees

I have a collection of phylogenetic trees produced from clustering DNA sequences, mostly a few nodes in each cluster/tree, with several clusters of size 1. And I would like to visualize them all ...
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2answers
102 views

16S species-level taxonomic assignment--what is the current state of the art?

We currently use DADA2 for picking ASVs and the assignTaxonomy funciton for assingment to genera. Google does bring up various recent articles on species-level ...
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2answers
107 views

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

I am trying to build a robust amino acid phylogeny with adequate robustness support (see previous post: How to make a robust amino acid phylogeny with adequate robustness support). This is a brief ...
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1answer
66 views

Weird phylogenetic tree

I am new to research. As part of my MRes, I am required to create a phylogenetic tree(s) of my genes of interest. I am currently blasting (tblastn) my genes of interest from S. mediterranea against ...
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2answers
55 views

Protein model quality assessment

How do I perform protein model quality assessment? I will obtain predicted structures from DMPfold, I-Tasser, and Rosetta, what should be the next approach to select a structure from among this set ...
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1answer
78 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)...
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2answers
149 views

PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...
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5answers
96 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 ...
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1answer
31 views

Calculating Unifrac Distance and missing data

I am trying to calculate unifrac distance for my OTU table, which has about 3000 taxa, and 300 samples. My phylogenetic tree only considers the most important 500 taxa. My questions are: Do I ignore ...
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2answers
196 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 ...
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2answers
49 views

Inferring a phylogenetic tree from BLASTn

I am trying to infer a phylogenetic tree from a Blastn output and from what I have understood, what I should do is 1) extract the alignments and re-align them using Muscle, then 2) feed the .aln file ...
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2answers
300 views

How to find common sequences among 6 multi-fasta files

I have 6 multi-fasta files, every of them contains ca 1500 sequences like that: ...
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1answer
75 views

Are there any resources for calculating / representing evolutionary relationships within gene clusters?

I am working with a gene cluster found in several species. The genes involved are pretty much the same, with the odd insertion, but they can be often found in different orientations. So, I can't just ...
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1answer
45 views

Visually summarizing phylogenetic networks

After having worked with Bayesian phylogenetic tree inference for some time, I am now trying out a method to infer network phylogenies. To get an idea of what it infers, I'd like to find a way of ...