Questions tagged [phylogenetics]
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
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How come bigWigSummary shows coverage greater than 1 for some region of the genome?
I am running this command, using the UCSC utilities:
bigWigSummary -type=coverage ./galGal6.phastCons77way.bw chr4 25526708 25528708 1
to get phastCons77way ...
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Using average of sequence similarities when delimiting genera - how to deal with outliers?
Sometimes I am trying to see where a (bacterial) genus ends and where another one begins based on 16S rRNA phylogenies. Of course, the length and support of the branch matter a lot, but this question ...
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Genetic relationships between Cyanobacteria: terrestrial vs aquatic
I believe one of the site members is an expert in Cyanobacteria hence the question.
I'm looking for a comprehensive 'phylogenetic tree' of the phylum Cyanobacteria and want to identify all the ...
M__♦
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Scale on the y-axis in a tree rotated with 'layout_dendrogram()' using ggtree
I'm editing a time-scaled tree using ggtree. The dates are correctly adjusted when I apply the 'mrsd' command and 'theme_tree2()', but when I try to rotate the tree with 'layout_dendrogram()', the ...
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phytools add.species.to.genus could not match your species to a genus
I have a species tree to which I am trying to add species, which includes a tip "Geissospermum laeve". When I run:
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Finding linkage disequilibrium when I have a kinship matrix but not pedigree
I have a bunch of samples of a non-model organism divided in two groups: parental generation and offspring. I do not have a pedigree so I do not actually know who is a parent of who, and which are the ...
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Correlation heatmap of RNA-seq clusters all samples together leading to very low no. of DEGs
I am writing to you to take an input or may be you can provide a different perspective. I am at wits end :(
So I have nearly 200 samples. These are separated into two groups (group I treated with ...
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Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average
I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine... except some of the codon ...
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How to determine the phylogeny of a specific set of genes
My goal is to understand the phylogeny of genes involved in bacterial restriction-modification systems, in psychrophilic bacteria.
To do so here is what I have done.
Downloaded the protein sequences ...
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How to parallelize BEAST
I'm running BEAST v1.10.4 with BEAGLE v4.0.0. My dataset has one large partition and I have access to a machine with many CPUs so I would like to optimize performance by parallelizing the process. ...
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Phylogenetic tree from a large FASTA file
I want to create a phylogenetic tree using a 3.8MB FASTA file with ambiguous code. How can I perform multiple sequence alignment and the construction of phylogenetic tree with these ambiguous codes?
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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 ...
M__♦
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NCBI Blast databases - cannot find some databases
I'm working with a system that does local BLAST searches using some preconfigured BLAST databases. From what I see, these were updated within the last year, but I cannot find any current databases ...
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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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compare fasta sequences in pairs and collect metrics
I have 96 fasta files (A1, A2, A3...) from one plasmid assembly pipeline, and I have another 96 fasta files (B1, B2, B3 ...) from another plasmid assembly pipeline.
I would like to compare pair ...
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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 ...
M__♦
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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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Why is COI metabarcoding not used for prokaryotes?
I'm a beginner in bioinformatics working with environmental metabarcoding, and while reading up on different marker genes, I understand that COI is preferably used for animals thanks to its higher ...
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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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Should I compensate for two clusters of samples in microarray by hierarchical clustering and MDS?
I seem to have two groups of samples based on hierarchical clustering as well as MDS plot analysis using the sample label from the tree cut of the hierarchial clustering. I am analyzing microarray ...
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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 ...
M__♦
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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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