Questions tagged [phylogeny]
Phylogeny is a statistical approach for reconstructing evolutionary relationships using trees
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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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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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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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Calculating total number of Unique gene in every genome from ROARY pangenome output
I performed a ROARY from 100 genome. I got several file including gene_presence_absence.csv from the results. I want to know how many unique gene(unshared gene, based on blast homology, same gene (...
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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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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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What do you use the CLANS program for?
I am reading this paper called Birth and death in the Terminal Complement pathway, doi : https://doi.org/10.1101/2022.04.21.489004 where they have performed CLANS analysis.
I understand that CLANS ...
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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 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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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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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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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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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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difficult in runing the R code for ggtree
I tried to run the below code but ended having issue. I have checked thoroughly and I didn't find any mismatch in fasta sequence
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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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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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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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How to align integer (non-DNA/protein) sequences?
I am looking for an algorithm to find the "best" alignment between two sequences of integers similar to how one aligns nucleic acids or amino acids for homology comparisons. For example, the ...
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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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ggtree：How to keep leading zero ‘0’ in the tiplabel？
I am using ggtree to draw a phylogenetic tree.
Some taxa IDs have a 0 at the beginning.
However, when I plot the tiplabel the leading zero is automatically dropped. ...
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Phylogenetic tree building from proGenomes database for shotgun metagenomics
For some weeks I'm fighting with an issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account phylogenetic distance.
I’m ...
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Phylogenetic tree rooting in shotgun metagenomics
But I have some weeks fighting with this issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account tree distance branches ...
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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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What can be the reason of getting negative branches lengths after BEAST analysis?
BEAST2 is currently being used for tree reconstruction prior phylogeographic analysis. The sample size and loci are described below.
I thought that BEAST/BEAST2 does not allow negative lengths of ...
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Missing ',' in line when Biopython reads a nexus tree
I want to edit a tree that I got from BEAST2 treeannotator in nexus-format.
Usually I use the module Phylo from Biopython for such work but ...
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Help me to calculate Heaps Alpha value from the roary pangenome pipeline result?
I need to know whether my pan-genome is open or closed. For that, I need to calculate the ...
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Is it possible to reconstruct an MSA with PSSM?
I am thinking of reconstructing an multiple sequence alignment (MSA) of protein sequences from a position-Specific Scoring Matrices (PSSM).
Is it possible? I suppose co-evolution information is lost ...
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How to use GEO_SPHERE?
I have some problems with geosphere package which extends/applies the Beast Bayesian MCMC package for calculating phylogenetic trees. Please, could anyone give any hints about at least one of them?
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Questions about microbial 16s rRNA phylogenetic, ANI Taxonomy, and GGDC
I have a few questions about these three methods.
We commonly use 16s rRNA to identify species and construct a phylogenetic tree. If there's a new isolate from a new and undiscovered ecosystem, ...
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Hirschberg's Alignment Algorithm Implementation. Works on the wiki example but not on large sequences of dissimilar size
I implemented Hirschberg's algorithm in python and used the wiki example to verify correct implementation given the scoring parameters and sequences:
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Protein-coding gene evolution age and species divergence time: are they correlated?
Is it possible to infer protein-coding gene evolution age by species divergence time?
For example, species A diverged 300 million years (MYA) ago from its common ancestor with species C, whilst ...
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Bio.codonalign.codonseq module (cal_dn_ds) for SARS-COV-2
I have calculated the dN,dS ratio for a SARS-COV-2 data set ('NC_045512.2' (Wuhan strain) and 'LC666924.1'), and results in a zero value (for most of the genes).
Is it possible and what is the ...
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No bootstrap value on single-copy gene tree created by OrthoFinder
I'm running analysis with OrthoFinder and it produces a single-copy gene tree. When I visualize the tree with iTOL, there's no bootstrap value on the branches or nodes. There's a published paper in ...
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Mapping NCBI taxID to divergence time?
I want to map NCBI taxID, specifically a pair of Genbank sequences, to the divergence time estimate of their common ancestor. For example, using a coalescence theory approach predominantly used in ...
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What is the most appropriate way to find the most recent common ancestor between two distantly related species
I want to specifically find the common ancestor between a lobster and a humans. I suspect it was an aquatic worm of some description. But I want to know about the nervous system of this common ...
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What exactly is a reasonable evolutionary criterion? [closed]
I got a rejection of publication which the reviewers mainly point out as not following a reasonable evolutionary criterion for choice of species used for phylogeny creation. In our dataset, a list of ...
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Simulation of DNA sequences through substitution rates
I'm looking for a little bit of guidance.
My question is regarding the simulation of DNA sequences with a fix substitution rate.
The majority of the programs for simulating sequences use Continuous ...
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Constructing a phylogenetic tree for classical MHC genes from different organisms
I am interested in constructing a phylogenetic tree containing the classical HLA α1 and α2 domains and potential classical MHC α1 and α2 domains of a different organism. I am using the amino acid ...
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Tool that can sort NCBI taxonomy ids based on phylogeny
I have a set of NCBI txids (of varying ranks) that I want to sort in some way (e.g. a table or a tree, the way it is sorted isn't super important), based on the current NCBI data for phylogenetic ...
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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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