Questions tagged [phylogenetics]
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
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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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Is there a DNAWeaver How-to guide?
Recently I've been trying to use DNA Weaver for customized gene assembly design.
Although there is a web version that allows to perform some assembly examples, I've tried to replicate them with python ...
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How are BLAST record scores calculated in biopython
Can someone explain how the score is calculated for Bio.Blast.Record.Description? For example, if Record.Description.num_alignments is >1, is ...
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Improving list speed: glycosylation example
I discussed a question with @gaspanic Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions
. The issue emerged was speeding up lists in Python. ...
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reverse translation from amino acid string to DNA strings
what is the opposite of .translate() function calls ?
I mean let's say I am given an amino acid string CYCLIC, how do I obtain all the possible combinations of DNA ...
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RNA strings and amino acid string
Which of the following RNA strings could translate into the amino acid string PRTEIN? (Select all that apply.)
I am not sure if the following mass of amino acid is relevant to the question.
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Parsing text within a taxonomy.csv file
I have the following file in tab separated values (TSV).
ID
Taxonomy
76980f6d906c6baaef3f96559fc7ba1b
d__Eukaryota; p__Cercozoa; c__Vampyrellidae; o__Vampyrellidae; f__Vampyrellidae; g__uncultured
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Calculate interval of flanking introns
I am looking for a easy way to calculate the intervals of flanking introns based on a transcript annotation file. I have chosen a very complicated method:
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PCA analysis of samples in a phylogenetic tree
I have a phylogenetic tree.
Each branch ends have samples (s1, s2, ~ s16).
What I want to do is, I want to make PCA analysis plot for each sample.
First I thought each sample has each lineage (...
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How can I remove FASTA sequences with an asterisk inside the sequence?
I have several protein sequences with an asterisk in the middle of the sequence, and I'd like to remove those sequences.
In the example below, I have three sequences:
From this example, I would like ...
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R ggtree apply colors to branches with multiple colors
This question was also asked on StackOverflow
I have a phylogenetic tree made with a Newick format
((a:1,b:1):2, (c:1, d:1):3):1;
The output will be
I have drawn ...
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