Questions tagged [phylogenetics]

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

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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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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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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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Edit all the fasta headers using awk

kindly your comment highly appreciated have more than 4k header sequences look like: ...
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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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271 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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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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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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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
47 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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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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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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135 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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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 some relation with the the length of the shortest hanging edge but I can not figure out how this ...
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3answers
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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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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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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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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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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
75 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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PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...
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5answers
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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 ...
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Calculating Unifrac Distance

So I am trying to calculate unifrac distance for my OTU table, which has about 3000 taxa, 300 samples. Now my phylogenetic tree only consider the most important 500 taxa. My questions are: Do I ...
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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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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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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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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
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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 ...
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For phylogenetic tree construction from core-genome which one is preferable: amino-acid based MSA or nucleotide based MSA?

The genomes are from same species. Is it true that, in phylogenetic tree constructed from amino-acid based MSA (multiple sequence alignment) some information are lost, so for phylogenetic ...
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Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?

I would like to visualize tree with multiple sequence alignment. My din.newick file is shown below, ...
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Confusion related to effective population size

I am making a demographic model for African American population in which I say 80% of ancestry comes from African population and 20% comes from European population. I am using the time/population time ...
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1answer
187 views

What do negative dN or dS mean in cal_dn_ds in Biopython?

I'm noobie in bioinformatics. I use cal_dn_ds from Bio.codonalign.codonseq with method 'NG86'. Sometimes I get dS=-1. What does ...
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Evidence of emergence of “genuine” novel protein interactions by aa mutation [closed]

Anyone knows of an example of a protein that, without coming from a recent duplication event, underwent a mutation(s) that caused it to have a novel interaction with a new ligand, substrate, other ...
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232 views

What is the best argument for maximum parsimony method in phylogenetic tree construction?

Beside it (maximum parsimony) being compuationally cheap what other good arguments are there for it? Is there any model behind this principle ? Why would one expect this principle to provide right ...
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113 views

Crossover question from Coding Theory

I have a model that, for a given bit of code will produce a binary string. An example is given 01010101, it might produce {1,11}, and given 01010000, it may produce {2, 11}. I have a lot of these ...
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Are phylogenetic tree construction algorithms any different than general clustering algorithms?

I suspect the answer is no. But I don't know enough to be sure that that is the case. Of course phylogenetic tree construction uses biological knowledge, e.g special distance metrics, but does it ...
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How snippy makes MSA-like aligned fasta output from multiple samples?

From the log file it seems snippy doesn't do assembly. It only does mapping: fastq --> SAM --> BAM --> VCF --> consensus_seq/snps But if multiple ...
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1answer
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Help interpreting my phylogenetic tree construction of bacterial species in same genus

I constructed a phylogenetic tree using mole blast, and it created a neighbor joining tree, so I used the alignment of those sequences with mine (1-43) in mega with TN93+G+I model but I don't ...
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Common Mouse and human DEG analysis

I have DEGs from human and mouse (equivalent of a human disease model), and would like to generate a logCPM correlation plot between the overlapping mouse and human gene (275 genes). Prior to ...
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How to create Phylogenetic Trees from fasta files in Python or R?

Given around hundred fasta files with DNA sequences with good coverage, how could I create a Phylogenetic Tree from it? Ideally in python or R. I found Phylo from <...
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Calculate the percentage of each unique phylogenetic tree in a BEAST output

I have a nexus formatted BEAST output containing 20,000 phylogenetic trees of seven taxa. Is there any way to get the percentage of each unique phylogenetic tree contained in this output? I already ...
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Perfect Phylogeny vs Maximum parsimony

I am searching various sources about phylogenetics. I saw some materials about perfect phylogeny and also phylogenies acquired from maximum parsimony constraint. They seem very similar to me. Are they ...
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Truncating branch length values of Phylogenetic tree with biopython

I have been using biopython 1.72 to display my phylogenetic tree files. 1)Using the function 'Phylo.draw(pars_tree, branch_labels=lambda c: c.branch_length)' to ...
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mrbayes, Sumt ; Error when setting parameter “Filename” (1)

question 1 I wanted to use sumt command after completion of mcmc run. Whenever I use, sumt Filename=infile.nex, it gives me the error: ...
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How do I interpret the function O(f^-2 log n) in Shekhar et al. (2017)?

The results of Shekhar et al. (2017) "indicate that ASTRAL requires $\mathcal{O}(f^{-2} \log{n})$ gene trees to reconstruct the species tree correctly with high probability where n is the number of ...
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MrBayes runs as single-core, but hangs when multi-core

I successfully compiled MrBayes v3.2.7 from github, with the configuration options ./configure --without-beagle --enable-mpi. The program is called mb. I tried one ...
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282 views

What is outliers and how to determine outliers in the following phylogenetic tree?

I confused with the term 'outlier' and 'outgroup'. Could someone explain with the example phylogenetic tree above? Thank you very much !!!
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Does the “.full.aln” file produced by snippy-core contain all bases of my input sequences aligned to the reference genome?

I have a number of sequences and a reference genome. I used snippy to align each individual sequence with the reference genome. I then used ...
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How do I interpret my phylogenetic tree construction from Glucosidases in the Actinobacteria class?

Dear knowledgeable bioinformaticians, I'm currently pursuing an undergraduate degree and as a result I do not have so much knowledge in this topic. I'm having some troubles understanding my ...