Questions tagged [phylogenetics]

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

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26 views

Relaxed and sequential Phylip format conversion

I routinely use AlignIO in BioPython for manipulating alignments and in context here moving from fasta format to phylip format. Alot of phylogeny packages accept a relaxed (sequence ID) & ...
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32 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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40 views

Finding out-group in unrooted tree

Im trying to find the out-group in the alignment my data files file a and file b both the case i'm getting NA when i run this ...
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23 views

Removing stop codons from alignment file for dn/ds calculation

This is one of the question which is very similar to my problem or almost same to my problem I ran with dummy data nucleotide alignment and the amino file it works perfectly fine,i can run the dn/ds ...
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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") ...
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44 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 ...
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32 views

Motivation behind the neighbor-joining distance matrix recomputation

In each iteration of the neighbour-joining method of phylogenetic trees construction, after joining the nearest neighbours the (additive) distance matrix $D_{m \times m}$ is recomputed as $$d_{ij} = (...
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4answers
168 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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16 views

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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17 views

phangorn fasta file read error

Im trying to read a multifasta sequence file into phangorn I get the following error ...
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29 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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35 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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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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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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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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32 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
78 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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64 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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25 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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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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119 views

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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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
75 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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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
30 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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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
110 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 ....
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119 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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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
105 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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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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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: ...
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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 ...
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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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327 views

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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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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435 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
61 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
34 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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111 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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49 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
860 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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60 views

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 length of the shortest hanging edge, but I can't figure out how this works.
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4answers
131 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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3answers
122 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
124 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
67 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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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
79 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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158 views

PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...