Questions tagged [phylogenetics]
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
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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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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 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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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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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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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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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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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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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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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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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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Is there a graphical/interactive 16S rRNA clustering method?
I've been doing phylogenetics with large (hundreds) 16S rRNA sequences lately.
Usually I'm focusing on one order, and using a combination of trees and sequence similarity to assess stuff like 'is this ...
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Phylogeny building in R from FASTA files:
Im working on building a phylogeny from scratch with downloaded FASTA sequences from GeneBank. I think Im doing alright up until the multi sequence alignment in the ...
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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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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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Is there a way I can combine geological data with population genetics data?
So I have ran SAMOVA and made calculations regarding haplotype diversity and nucleotide diversity of several populations. I have also made raster data regarding geographical data like slope, ...
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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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Where can I find the FCT value after running samova?
I have ran SAMOVA 2.0 for 2 groups so far. I want to determine the right number of groups and I know that the correct way is to run it more than once with a different amount of groups and then check ...
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Read Clustal file in Python
This question was also asked on StackOverflow
I have a multiple sequence alignment (MSA) file derived from mafft in clustal format which I want to import into Python and save into a PDF file. I need ...
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How can I fix "Ill-defined genetic structure" Error message in Arlequin?
I am performing an AMOVA analysis via Arlequin.
At this point, I have:
collected sequences of mtDNA from the cox1 gene,
aligned the different genes using clustalX
converted the files into .arp ...
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How can I use sequences with different lengths in arlequin?
I have mtDNA sequences of the cox1 gene from various populations of one species. I want to perform an AMOVA allele frequency analysis via Arlequin. This allele frequency package however requires my ...
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How can I resolve "missing name of population" message in PGDSpider?
I want to use Arlequin for AMOVA. I have my FASTA files which I want to convert into .arp files which are recognizable by arlequin. When I try to convert it using Population Genetics Data (format) ...
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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 make unrooted tree for Likelihood mapping result by using IQ2-tree?
I am a biologist, and I do not fully understand the tree topology of the experimental species.
I used four-taxon set (4 sequences) to identify the Four-cluster Likelihood-Mapping by using
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Downloading genes from NCBI in fasta format
I'm pretty new in bioinformatics.
I need to download FASTA sequences of several genes. The list of genes I have assembled consists of 140 genes, so I'd rather do this through via code than download ...
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Maximum likelihood estimation for tree construction
Could someone direct me to a resource (textbook chapter, lecture notes, online video, etc.) that demonstrates, in a mathematically or computationally rigorous way, how to use maximum likelihood ...
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segmasker doubles found intervals
During NCBI BLAST+ segmasker output exploration, I found out that for some sequences, the program returns the same interval twice:
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Why does segmasker modify headers?
When parsing NCBI BLAST+ segmasker output, I realized the program modifies almost every header containing these strings: ( or )...
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How to wget a gff from NCBI database?
Say I want to use wget to download a gff file for the X chromosome of release 5.57 of the Drosophila melanogaster genome. The NCBI page with the gff file for just this is here.
However, I do not see ...
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finding the frequency of a motif-matching peptide
This question has also been asked on Biostars
I want to find the frequency of each motif-matching peptide.
The sequences are:
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How to identify mutations in a viral genome
I have a fasta file with multiple sequences comprising 38 sequences. The length of the sequences are around 11000 bp.
How can i get changes in the genomes based in a reference genome? (aa subtitutions ...
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ETE4 manual or improved code description
ETE3 * (Environment for Tree Exploration) is a major package and in particular Python package to navigate phylogenetic trees. It is the premier coding library/package for tree manipulation.
ETE4.0.0 ...
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Converting Pairwise single- linkage clustering distance data to "newick" format
I have pairwise distance data for single linkage cluster and I would like to convert it to newick format.
I was unable to find a conversion algorithm.
I require newick format for visualization and ...
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Compare and Reorganize Fasta Headers Python
I want to compare the headers from the fasta file to file1, and if there's a match, reorganize the header and put the match first. If there's no match between fasta file and file1, look at file2 and ...
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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 align two novel sequences to a reference genome and build a phylogenetic tree?
I have two new amino acid gene sequences that I want to align to a reference genome. Is it a good idea to have a combined phylogenetic tree? what will this type phylogenetic analysis called?
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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 get full headers with tabs as separators with segmasker?
I try to pass a .fasta file with headers where tabs are used as separators as input file to NCBI BLAST+ segmasker:
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Add file name to FASTA file header using SeqIO
I have several fasta files that represent the proteins from different orthogroups. However, the orthogroup that each of the proteins belongs to is not indicated within the files. I am leveraging ...
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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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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 to merge multiple list into a single dataframe replacing common values with 1 -python
I have multiple lists on python:
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I want to map TFBS on to the sequences from dataset containing 8448 (210 base) sequences. its not giving all the hits I need
I want to map TFBS (transcription factor binding sites) on to the sequences from dataset containing 8448 (210 base) sequences, but it is not giving all the hits I need
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Single or partitioned model for supermatrix tree inference?
I am dealing with several genes in my dataset. For each of the genes, I have built gene tree, with their best estimated model. I am intended to look into the effect of the tree from concatenated ...
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Fixing FASTA file for Local BLAST Database
I recently prefetched 157 SRA files from an NCBI BioProject using the SRAtoolkit. I then used the toolkit to download those files in FASTA format.
Each individual FASTA file looks something like this:
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How does one distinguish nuclear DNA from mitochondrial DNA when doing WGS?
I'm interested in doing de-novo sequencing but also phylogenetic analysis. In particular, after de-novo sequencing and annotating the genome, I need to align the CO1 gene and the nuclear 28S rRNA gene ...
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drawing multiple sequence alignment as tree in R
I am very new here. Please help me with my codes as am trying to draw multiple sequence alignment as tree suing ggtree package in R and i have following error.
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CLI access to genomes/proteomes by BioSample ID [duplicate]
This question was also asked on Biostars
I'd like to download multiple genome assemblies or proteomes using a set of BioSample IDs from NCBI.
I'm able to find the assemblies belonging to the BioSample ...
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