Questions tagged [phylogenetics]
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
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Select synonymous sites from a multiple sequence alignment
Could someone kindly recommend a tool or R package that can identify synonymous sites in a multiple sequence alignment?
I wish to select those taxa for tree reconstruction and other downstream ...
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Evolutionary tree from SNP data
I would like to make an evolutionary tree using the SNP data from DArTseq. Are there any software or packages available for this purpose? I came across the software SNphylo, but its home page is not ...
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How to use Gblocks for trimming single-copy gene sequences?
I have run OrthoFinder on a set of 11 genomes and got the results in a folder. From the output folder, I saved all the single-copy gene sequences in a single FASTA file and now wish to remove all gaps ...
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How to add bootstrap values to the phylogenetic tree generated by OrthoFinder?
When we run the OrthoFinder analysis tool on a group of genomes to get the orthologues shared by them one of the output files include a folder named 'Species_Tree' that contains a text file named '...
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How to get a GISAID account? I registered months ago, still no reply!
Inspired by amateur variant hunters, I would like to join the Pango lineage proposal community and help contribute to variant surveillance.
However, I cannot seem to get access to GISAID, the platform ...
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How to obtain desired output?
I am working on a project using the following command within nano:
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Genomics Statistics Problem
I have used a python script to identify target sequences in a DNA sequence file. There are two classes of sequence: coding and non-coding.
I have identified 728 sequences of interest. 597 of these ...
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Refactoring pandas using an iterator via chunksize
This question was also asked on Stack Overflow
Bioinformatics rationale eggNOG files can be very big and sump all available RAM for regular to medium sized desktops.
I am looking for advice on using ...
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Blast output file only shows 500 lines -outfmt 6
I had created databases of different sets of metagenome datasets - one with 6 runs, other with 48 runs, another with 100 runs, etc using the accession list for each of these datasets and makeblastdb ...
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Selection analysis based on each leaves as foreground with FastCodeML
I am using positive selection analysis for each leaves in a phylogenetic tree.
In the routine calculation via codeml, I will be running model zero for all leaves ...
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Pairwise alignment using CIGAR String
I want to perform pairwise alignment and get the resulting CIGAR string (Concise Idiosyncratic Gapped Alignment Report). A fuller description being here
The channel can emit insertions, deletions and ...
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Parsimony-distance neighborhoods in tree space
I have the following question about the paper A parsimony-based metric for phylogenetic trees by V. Moulton and T. Wu.
In this paper, the authors define a "parsimony-distance" between ...
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Pandas automatically rounds GWAS P-value
I am working with a specific GWAS. If I were to run this on the command line
grep <rs_id_of_interest> GWAS.txt
I would see the GWAS p-value to be on the ...
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Removing genes with less than a correlation cut-off between two matrices
I have two matrices like this:
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Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?
The SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it...
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DNA, molecular descriptors
Are there any programs (preferably command line tools) for calculating molecular descriptors of DNA? I am looking for something like Chemopy or RDKit but specifically for DNA.
Thanks in advance!
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How to identify all descendents of a branch on a phylogeny
I'm trying to simulate the evolution of binary traits on phylogenies in R to end up with a dataset of the traits held by each tip. Starting at the root, at every timestep, new traits are added with a ...
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Is it possible to do homology inference across species using different kinds of NGS data?
Background: I have a list of species that I want to put through homology inference. The goal of homology inference is to investigate the evolution of a trait on a species tree. I want to use the ...
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Merging ssu-align alignments
ssu-align is an HMM-based MSA tool for ribosome's small subunit (SSU) sequences. It's bundled with three SSU models:
archaeal,
bacterial
eukaryotic
Approach Given a set of archaeal and ...
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What datasets are available out there for prediction based on DNA sequences? [closed]
I am looking for publicly available data for a genomics deep learning project. My goal is to compare different architectures to predict biological insights from DNA sequences.
I have heard about ...
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How to find/build the evolutionary history of a protein from its sequence?
I'd like to build the evolutionary history of a protein, given its sequence. Namely, given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein as an example:
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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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What is the limit of partition incompleteness in Bayesian MCMC?
I am seeking advice on whether or not to incorporate incomplete data into my BEAST analysis.
I have HIV data consisting of two partitions of the pol gene: one that is 1.2 kb in length and present in ...
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Align the HIV-1 Gag protein with the Gag protein of Visna virus
Align the HIV-1 Gag protein with the Gag protein of Visna virus
Background Visna virus is a lentivirus causing encephalitis in sheep
The problem is align the follow two protein Gag of viruses HIV-1 (...
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Are there any Genome in a Bottle-like resources for non-humans (especially for invertebrates)?
Genome in a Bottle is an excellent resource that provides many types of DNA and RNA sequencing reads for a single individual/cell line to test genome assembly and analysis tools. For example there are ...
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Any suggestions for cultivar identification using SSR (simple sequence repeat) markers
This is the data I have now: 30 simple sequence repeat (SSR) markers for 80 cultivars of cucumber. 10 of the 80 cultivars belong to one cultivar (let's say A).
My goal is to classify an unknown ...
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What are the different kinds of bioluminescent genes?
I know of the common green glow gene but I forgot the name and I also know that some algae glow blue. There are so many types of bioluminesent organisms, so I am wondering what species have which ...
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UPGMA computation
The unweighted pair group method with arithmetic mean (UPGMA) is a hierarchical clustering method, for example used in phylogeny. In a phylogenetic tree it would result in a global molecular clock ...
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Can't load files into PopART
I am trying to create haplotype networks in PopART (Population genetics with Reticulated Trees*) which I have successfully done many times in the past.
Two weeks ago the program was working fine for ...
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Using information criteria weights to create consensus tree
While I am familiar with calculating information criteria for various ml models of a multiple sequence alignment, I am not aware of how to use the derived weights to create a tree that combines ...
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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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How to fix NameError?
I am working on a project and am having issues with the following code that I have written in nano:
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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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Using ticks on the x axis or a scale bar when visualisizing a phylogram?
When visuliazing a phylogram is it preferable to show ticks on the x axis or a scale bar?
Given an example tree with branch lengths in newick format ...
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How to interpret Mendelian randomization results?
I did Mendelian randomization using this software:
https://cran.r-project.org/web/packages/MendelianRandomization/vignettes/Vignette_MR.pdf
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How do I generate a variant list using Illumina reads from a Salmonella genome?
I am planning on performing phylogenetic analysis of Salmonella specimens using WGS data from PulseNet and GenomeTrakr, for the purpose of public health surveillance & to provide context for ...
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How to install DnaSP on a Mac
I need to install DnaSp, a nice GUI originally written for Windows for the population genetics of nucleotide sequence data.
However, its not working on my mac. I'm using wine to install it using these ...
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How can extract the list of genes name from the raw data in GEO?
The format of the raw data that upload in GEO is different, like TXT, CEL or other form. How can I extract the list of genes name from these formats? And then how can I normalize them with R?
I would ...
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How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?
I would like to download a number of SARS-CoV-2 fastas from NCBI/Genbank using a web endpoint. I looked on their website but it's confusing.
I have the accession numbers, but can't figure out how to ...
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Build tree to calculate beta diversity
I am trying to calculate beta diversity* using the UniFrac distance on my data, each sample having OTUs values.
To calculate it, I saw it required building a tree with percentages that represented the ...
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Loss of predictive power of polygenic risk score when dataset contains missing variants
I am trying to calculate polygenic risk scores (PRS) scores for a new dataset. This dataset does not have all the variants that the PRS score needs. The PRS score I am interested in has 40 variants, ...
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Using R `ggtree`, attach extra data next to the nodes on an illustrated tree/newick file
This is really a programming question but ggtree might be too obscure for this question to be posted on StackOverFlow as a general R related question.
I am having ...
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Retrieval protein definition from accession ID
I have a list of protein accessions:
XP_025107904.1
PVD22034.1
AJA37836.1
How can I obtain the definition of the protein, and the related organism?
Output:
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Is there a way to calculate the number of parsimony informative characters in a morphological dataset in R?
I have a dataset of binary morphological characters and would like to know how many of them are parsimony informative. Is there a way to calculate this with an R package?
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Plot phylogenetic tree from list of edges
I have a dataset that I wish to convert to tree or phylo format like in the ape package, in order to plot the phylogenetic tree. It is formatted like a list of ...
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Problem with setting fixed topology for MrBayes
I need to use partitioned DNA input (concatenated multiple genes) and fixed topology (species tree from ASTRAL) to get branch lengths in MrBayes. I have input NEXUS like:
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Math on Pandas Columns
I have a pandas dataframe that reads in a PAF file from minimap2. What I would like to do is take the first 5 columns of the data from to create a BED file.
I used this to extract the first 5 columns:
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How to promote assemblies into genomes in NCBI?
Note: I've never submitted an assembly/genome to NCBI, so excuse if my perspective is flawed.
I'm working with Drosophila subobscura. (spring fruit fly)
I see here https://www.ncbi.nlm.nih.gov/data-...
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How can I get data of single cell RNA sequence with raw count?
I am using dataset GSE85241, but I can't find the read counts of the dataset. It only provides with RPKM values.
How can I find the read counts of a dataset?
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eggNOG API, how's it work?
Background eggNOG uses seed orthologues which correspond to its own internal database, so for example J421_1876 can be placed in its online search engine here. This ...
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