Questions tagged [phylogenetics]
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
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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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Is there a software that can predict protein-DNA binding?
Is there any software that, given a DNA sequence as input, can predict what protein/ type of protein can bind to the DNA. The sequence of interest is a potential transcriptional regulator, I want to ...
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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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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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How can I extract all known mutations of my BAM (or SNP/INDL files)?
I am using a Genome Explorer tool to see all the mutations on my own DNA.
My particular interest is on listing the variants and get their names/ids.
Here are a few screenshots:
You can see that ...
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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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How can I convert codon coordinates to genomic position?
I am looking for a given mutation in IGV, which accepts coordinates in the form of
chr<X>:<Y>
Where X is the chromosome number and Y is the base ...
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Get regions' information from DNA sequence data (bsgenome.hsapiens.ucsc.hg19)
I have a problem in R. I have the following dataSet (the first three rows shown) (the 5th number is the methylation level in its region):
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How do I generate a list of post-synaptic gene markers that will guide me in my search for these markers in intestinal stem cells?
I would like to generate a list of gene markers that represent post-synaptic related genes. I will then use this list to search through single cell sequencing data, in order to assess whether certain ...
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How to query NCBI (Nucleotide database) by a feature qualifier?
I cannot seem to find a way to query nucleotide database (https://www.ncbi.nlm.nih.gov/nuccore) by a specific qualifier of the feature. For example, by /host under the feature "source".
For example, ...
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How to (efficiently) search nuccore to retrieve only annotated sequences?
I wish to efficiently search nuccore to retrieve only annotated sequences.
By "annotated" I mean that the nuccore entry contains annotation information.
An equivalent definition (if I understand ...
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Is there a built-in parser for the textual feature table that Entrez.efetch returns?
Entrez.efetch helpfully gives me the feature table of a nuccore entry.
If I understand correctly, efetch can only return the ...
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Generate an appropriate output from DNaSP6 to Arlequin program
I am performing a haplotype and nucleotide diversity analysis of my Sanger sequences (from Watermelon mosaic virus coat protein region) using the Arlequin program. My aim is to see the probability ...
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Primer-Blast Custom Database [error]
I'm using Primer-Blast to compare a PCR template against a custom database of reference sequences, using Primer-Blast's Custom database functionality.
However whenever I try to upload a FASTA file as ...
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Is it possible to go from a digital sequence to an actual nucleotide?
I'm trying to learn about what the state of technology is at presently. It seems like we clearly can go from nucleotide to digitally stored sequence, but can we transcribe something from the digital ...
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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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Downloading SRA Files from AWS
I want to download the original BAM files that the authors had uploaded to SRA. Normally, I would just use sam-dump, but the files are having issues that seem ...
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How do I pull singe cell RNA sequencing data from GEO database?
I am new to R and computational biology. I am trying to look through a published data set to check for gene expression for my own project. I am having trouble finding materials to teach me how to ...
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Problem with classification model of genomic data: every machine learing model predicts wrongly almost always the same subset of dataset
First of all, I'd like to apologize for any spelling or grammar mistakes.
I'm having a problem using R for a classification problem. My dataset contains ~300.000 genomic data, and the features are ...
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Unmapping Alternative reads in BAM file
I want to do some HLA typing, most of the tools require the bam file is aligned to primary genome without alternative read handling. From the International Genome Sample Resource project, I can get ...
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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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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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How can I classify the 3 clades(S, G, V) of the coronavirus without using protein data?
On GISAID they classified the coronavirus using 4 clades(S, G, V, Other).
I downloaded around 1,000 complete genomes of the coronavirus from GISAID and I would like to classify each one as belonging ...
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Theoretical limit of human genome compression
How small can a compressed file containing the human genome be?
I'm aware that this question cannot actually be answered, since it is asking for the Kolmogorov complexity of the human genome, which is ...
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Compressing the human genome to few megabytes
Multiple sources (see for instance this or this) discuss how genetic data will have scalability problems, given the huge file size of the human genome. The most straightforward encoding (see here) of ...
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Cannot blast against specific NCBI databases
I am having issues with some prokaryote reference genome databases (exact names : ref_prok_rep_genomes.*), that I downloaded from the NCBI website : https://ftp.ncbi.nlm.nih.gov/blast/db/. Files in ...
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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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Since every human has a different DNA (different combinations of C, G, A, T) what does it mean to have the genome done? [closed]
I'm confused about the difference between genome and DNA. Is it correct to say that the same type of bacteria has the same DNA? But my understanding is that it is not correct to say that the same type ...
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How to compute Shanon entropy
I want to analyze some viral sequences. I want to use shanon entropy as a measure to analyze the sequences. However I do not understand the concept of shannon entropy. Would anyone explain please how ...
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SRA run data access
Trying to download run data of Run accession SRR2155174. Here's the link: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR2155174
Please go to the link and go to the "Data Access" tab. Hereunder ...
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NCBI SRA database sample: control vs test
I was trying to download some data from NCBI SRA (SRA059451). There are 27 samples available for SRA059451. But i am unable to understand which samples are 'control' and 'test' samples. Please help me ...
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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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Translating a genome sequence into possible frames
I have a sequence below from MYC gene about which I need to translate the sequence in all possible frames AND identify (for each frame) which codons are actually used in MYC
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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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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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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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