Questions tagged [phylogenetics]
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
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Error while using E-utilities on slurm HPC
I keep getting the error while using E-utilities on Slurm HPC, could you suggest how I can resolve it?
SCRIPT:
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Comparing groups of 16S rRNA sequences - how to?
I have several groups of 16S rRNA sequences associated with taxonomic groups (let's call them A, B and C). The sequences within each group have a common ancestor and are on average more closely ...
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Add segregating sites to branches of a tree
I'm trying to figure out how I would plot a tree with number of segregating sites on display on the branches
I'm using acctran from phangorn to plot a parsimony tree (using phydat object from fasta ...
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How can I run the fdnadist command from the EMBOSS package?
My operating system is Mac OS X.
I would like to compute DNA distances between different sequences. For this, the dnadist package from the Phylip software would be good but hard to automate. EMBOSS ...
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BioJava - Protein to DNA
Using Biojava 5, I am trying to convert a sequence of Amino Acids to a Nucleotide sequence. Any idea how to do this?
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Does NCBI's blast API block my IP?
I am trying to run a blatn command from both my laptop and within a google colab notebook. I am not sure why, but this command runs properly once and then, on the ...
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Populations genetics and dynamics of bacteria on a Graph
Disclaimer:
I'm a physicist and I'm fairly new to Bioinformatics therefore somethings below may not make sense.
My purpose:
I would like to simulate genetic evolution of bacterial populations, ...
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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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Biohackers Netflix - DNA to binary and video
I'm not sponsored or anything, just interested in their challenge to decipher their DNA code.
They encoded their first episode of "Biohackers" video/binary file to DNA code and said if we ...
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Tracing and quantifying inheritance over many generations
Apologies if this is the wrong location for this question, and please feel free to point me in the right direction with appropriate Anglo-Saxon embellishments...
I'm after some ball-park numbers for ...
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Greedy Motif Search [ Reasoning ]
I was able to execute the algorithm correctly. But I'm still trying to get a hold of the result I'm achieving.
This is the algorithm I'm trying to understand -
http://rosalind.info/problems/ba2d/
If ...
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STRUCTURE interprets pop ID as locus
I'm using structure for the first time and I fail to execute a "job". For some reason, structure interprets the ...
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Need a alternative or more complex version of venn diagram in python for matching dna sequences
I am in google colab and I have combined and set up a data frame list of sequences that goes like this
Location ID Sequence
1.1 ........ A ........ AAGAGATA
1.2 ........ A........... ...
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Unable to use phangorn::phyDat
I am following an example from ‘Analysis of Phylogenetics Second Edition and Evolution with R’ from Emmanuel Paradis.
He is doing:
I am doing pretty much the same:
...
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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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How to assess if this strategy is good to have some phylogenetic information?
I have several organisms and I want to calculate for each one of these their codon composition implementing a pairwise distance matrix between these codon vectors to build a phylogenetic tree. ...
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How to modify DNA evolution model to fit actual data?
I'm working on understanding the evolution of a gene in a phylogenetic tree. I know the rates of evolution of each organism (from the tree).
I am taking a random DNA sequence with my gene, evolving it ...
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Time for running ADMIXTURE analysis
I am trying to run the ADMIXTURE software for the first time to analyse the structure of an in-house dataset of samples comparing to 1000 genomes project ancestral populations. I am trying to ...
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Does the kinship and inbreeding coefficients depend on population frequency of an allele?
I am reading Section 5.2, Kinship and Inbreeding Coefficients, of Kenneth Lange, Mathematical and Statistical Methods for Genetic Analysis. There the kinship coefficient $\Phi_{i,j}$ is defined for ...
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Extracting all information about a sample when using xtract from e-utilities
I would like to extract all information about each SAMPLE after running the following query (run the query and add a ...
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Power calculation for GWAS/EWAS
I want to investigate, how much sample size i needed to obtain 80% power for GWAS/EWAS studies. Phynotype trait is discrete (not case/control) for human disease.
I wonder, does anyone has came across ...
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Transcribing DNA exons and append transcripts into a list
I am trying to find a way to read and transcribe a list of DNA sequences (list of lists) only when the for loop finds a start codon (triplet of the list items) and until it finds a stop codon, over ...
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"How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree?"
I apologise for very basic question but I am very new to biology and have very specific knowledge of this field, I am currently working on Bioinformatics in my machine learning project which is why I ...
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Understanding the fasta file format and using edit distance for alignment
I'm a computer scientist teaching algorithms development in the Fall. One of the algorithms we teach is called Edit Distance, and our folklore is that it is used to compare RNA sequences (is this ...
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How to retrieve the DNA sequence from a particular species and region through command line?
I am new to working with the NCBI database so I am not sure how trivial this question is. I wanted to get DNA sequence of a specific version of the Xenopus tropicalis genome of a specific region (ie 1-...
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How to extract metadata from NCBI's experiment?
I want to extract metadata from experiment SRX1596422. I have sratoolkit and Entrex direct but not sure what line of code to use. Here's the link for the experiment: experiment SRX1596422
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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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Kraken2 > OTU format > Phyloseq
A collaborator has passed me over Kraken2 outputs *.report and *.kraken, from a metatranscriptomic sequencing experiment conducted on the minION.
I would like to make a tree if the data using a ...
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DiffBind, diffferentially binding site
I have data for 3 histone marks (2 for silencing and 1 for activation) each mark has three replicates.
when I run the diffBind package I have three contrast:
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Too many requests error when querying NCBI
I keep getting a "too many requests error" when querying the NCBI SRA database, even though I'm running less than 10 requests per second, and I have an API key, which supposedly should allow ...
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Programmatically retrieve Accession List from NCBI
I would like to programmatically retrieve the file "Accession List" from an NCBI page.
I'm running firefox, so I'm clicking the file and clicking Ctrl + <...
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Coding vs non-coding DNA length
I am trying to calculate the total exonic length (in bp) in order to see where the coding-noncoding ratio of roughly 1% to 99% comes from.
We know all chromosomes total about 3 billion base pairs. So ...
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e-utils api: get chromosome position for each snp on a gene
So I have the following e-utils api-link:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=5726&retmode=json
it returns all the SNP-ids for the gene with ...
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BWA: Detecting Variation between Reference Genome and Short-Read Sequences
I need to identify all loci in the short-read sequence at which the number of microsatellite repeats (i.e. number of copies of "AA," "GTC," etc.) differ from the reference genome, ...
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How can I obtain a list of all NCBI gene ID's along with their full name, symbol, and also known as symbols?
I would like to do two things:
(1) Obtain a list of all NCBI (Entrez) gene ID's.
(2) Obtain the "Official Symbol", "Official Full Name", and "Also known as" fields from ...
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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) & ...
M__♦
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Calculate Entropy for DNA Multiple Sequence Alignment in R
I am pretty new to R. So I apologize for asking maybe a very basic question.
Let's say I have a fasta file with sequence below:
...
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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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Encoding a 15bp DNA sequence into a shorter than 15 digits number
I have a series of 15bp DNA sequences from single-cell barcodes and I would like to encode them into a shorter than 15 digits number so that each unique 15bp DNA sequence will create a unique numeric ...
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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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How many markers or loci are used in forensic DNA profiling and the effect of the DNA sequencing?
I am reading the Wikipedia page on DNA profiling, specifically STR analysis. It says that DNA profiling relies on matching 20 or so loci. It also gives an account of finding false identification. But ...
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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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Generating taxonomic hierarchy by species/genus name
I am attempting to create a reference library of DNA plant barcodes in the ITS2 barcode region for plants from a specific region (Panama). I downloaded all the sequences for plants that resulted in a ...
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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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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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What steps should I follow for DNA analysis, for a classification problem?
I have a bed file which contains DNA sequences information as follow:
**
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Determine if an organism is microbic or unicellular
I am doing some metagenomic analysis of samples which can only contain microbes due to the experimental setup.
For this, it would be useful to be able to distinguish whether a specific organism is a ...
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mining DNA barcodes from Genebank/BOLD per location
Is there a method to download all the sequences for a particular geographic region (Panama) for 'DNA barcode' sequences (ITS2, rbcL or trnL). Hopefully, the specimen collection location will include ...
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List of global ethnicities
Looking at the 1000 genomes project I see the following list of population groups and super-groups:
https://www.internationalgenome.org/category/population/
However, is there something like a ...
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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
$$Q_{ij} = (...
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