Questions tagged [phylogeny]

Phylogeny is a statistical approach for reconstructing evolutionary relationships using trees

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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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  • 41
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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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1 answer
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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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5 votes
1 answer
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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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Does the alignment need to be redone when using SAW method to test long branch attraction?

I am looking into different methods to test the long-branch attraction problem. In this chapter they talk about the SAW method - excluding one and the other taxa from the dataset and see if they ...
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How to get phylogenetic tree from multiple genes?

I constructed a phylogenetic tree using a gene (example - secA). I had to gather the same gene sequence for all the required species from public database-NCBI and then constructed the tree after ...
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calculating phylogenetic tree from pairwise distances

I have a file with a 3-column list of pairwise distances: A B distance A C distance B C distance ... And I would like to calculate a phylogenetic tree for all the ...
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1 vote
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What is the tP statistic from ANGSD?

We were looking for genetic diversity in the exon level of an MHC transcript and analysing the data under ANGSD (Analysis of next generation Sequencing Data) written in C++ We used ANGSD to calculate ...
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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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How to decide whether to assume 2 Gene Losses or 1 to find minimum cost trees for Gene Duplication/Expression events?

This paper introduces an approach to estimate a convergence from discord between phylogenetic species trees and gene trees, using Gene Duplication and Expression events. A Gene Duplication (GD) event ...
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Computing Maximum Agreement Subtree of two unrooted phylogenetic trees with PhyloNet?

I am using PhyloNet to compute the MAST of two unrooted binary phylogenetic trees but I am not getting the output that I should. I think the issue might be with the way I am writing the trees in the ...
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3 votes
1 answer
26 views

Tajima-Nei Distance estimate with BioPerl

I have been trying to estimate Tajima-Nei distance for my data (link below). The output is s phylogenetics distance (pairwise) matrix which accommodates a detailed transition transversion and the ...
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Mrbayes stop at certain generation without error

I am using Mrbayes v 3.2.7 MPI version to infer phylogeny, and I set the ngeneration to 10,000,000, but it often stop at certain generation (usually far smaller than given generations). Even if I ...
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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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How to import a phylogenetic tree (in nexus format) with node support values in R

I have a phylogenetic tree in nexus format that was generated with RAxML. In the tree file, there are node support values. I want to plot this tree in R with the support values showing. However, when ...
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2 answers
74 views

Create a NHX phylogeny format with r or python

I need help to add information in my phylogenetic tree on each branch. I have two pieces of information at my disposal: A phylogenetic tree in newick format : (mammal:0.14,turtle:0.02,(rayfinfish:0....
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Dataset showing evolution of gene

As a way to exemplify how the hierarchical clustering of particular DNA sequences can be used to derive phylogenetic trees, I'm looking for a (even very small) dataset of the same genes (or other ...
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2 answers
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Consensus on how to select SNPs for creating a phylogeny when the full dataset is too large

I have got a quite large VCF file (about 20k samples with 160k SNPs after filtering for quality etc.) and I would like to get a phylogeny for it. However, the whole dataset's too large for my ...
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What is the origin of HIV1?

What is the origin of HIV1? This is the alignment of a small part of the POL protein of the HIV1 virus GenBank KU749412.1, with the POL protein of the Visna virus GenBank L06906.1 ...
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Analyzing and visualizing metagenomic data

I am starting out in metagenomics, Aim I wish to understand the whole analysis from the raw reads to interpretation. Background My current pipeline is used for: analyzing human gut microbiota cleans ...
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2 votes
1 answer
120 views

Plot information stored in dataframe within a tree (ggtree)

Hello to the entire Stackoverflow community! I'm writing to you because I'm currently building a phylogeny with ggtree and I have in parallel a table like this one: df : ...
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1 vote
1 answer
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Measure the purifying selection for certain taxa along a phylogeny

I am posting this message because I need clarity about the analysis I want to perform. In my analysis, I have a homologous gene in 13 species, and I would like to evaluate the selection pressure of ...
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1 vote
0 answers
49 views

Comparison of phylogeny of SARS2 whole genome vs spike genome

I’ve built two phylogeny at minimum evolution in MEGA-X and extracted these as newick files. My next step is to compare the two phylogeny to look at if the mutations within SARS2 are more prevalent ...
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1 vote
2 answers
383 views

Download complete Phylogenetic Tree as JSON

I would like to integrate the phylogenetic tree into a website. Does anyone know where I can download the complete tree? Best would be a JSON, which looks something like this: ...
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1 answer
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panic: division of zero by zero or infinity by infinity error when running GODON positive selection analysis

I am using godon to find genes under positive selection with the branch-site test. However, after running for a little while I get the error "panic: division ...
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1 vote
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GCF VS GCA or combination of both for pangenomic studies

I have just started to learn bioinformatics and pangenomics. So if this question seems to you pretty basic then I apologize in advance. As we know, NCBI for the genome database, there are two kinds of ...
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1 answer
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how to estimate phylogeny without DNA sequences?

I am new to bioinformatics, I am reading ‘Analysis of Phylogenetics Second Edition and Evolution with R’ from Emmanuel Paradis. I can create phylogeny from DNA sequences, by first calculating the ...
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0 votes
1 answer
72 views

Minimal working example for phylogenetic tree construction in R using an alignment of DNA strings and a vector of names?

I am looking at how to build a phylogenetic tree in R from aligned genetic information (dna sequences). There are multiple ...
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1 vote
1 answer
72 views

Standard for when to collapse phylogenetically uninformative nodes

I have been creating phylogenetic trees using RAxML (using Boostrap + ML) and I end up with a bestTree file, outputted in newick format. When I open up the tree in FigTree, I notice that it collapses ...
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1 answer
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What does instantaneous rate matrix mean?

PhyML is a tool used for maximum likelihood estimation analysis. I was running a PhyML analysis to check the rate of nucleotide change in DNA sequences and in the PhyML output, there are rate ...
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1 vote
1 answer
186 views

Adding external annotation to the phylogeny tree

I was looking to overlay annotation on my phylogeny made,which was solved here question asked where i was looking to compare two different phylogeny which i could do. Now i want to label the tips ...
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1 vote
1 answer
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Why does the Genbank phylogenetic tree of 4000 sars-cov-2 sequences only display 200 nodes?

I manually selected all 4000 sequences on the 20 pages of the SARS-CoV-2 sequences on genbank here. When I click on Build phylogenetic tree, it only has 200 nodes. ...
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1 answer
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Generate an appropriate output from DNaSP6 to Arlequin program

I am performing a haplotype and nucleotide diversity analysis of my Sanger sequences (from Watermelon mosaic virus coat protein region) using the Arlequin program. My aim is to see the probability ...
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