Questions tagged [phylogenetics]

Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.

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Construct phylogeny from a Fasta file

I have a set 189 taste receptor protein sequences (not aligned) in a fasta file. I like to get the phylogenetic tree in newick format. I was using earlier https://ngphylogeny.fr/. Unfortunately now it ...
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1 vote
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Should I expect / use a prokaryote-specific substitution model when building a phylogenetic tree?

I have a couple of prokaryotic genes that I'm trying to build phylogenetic trees from. I inputted them into IQTree, which, as part of the workflow, runs through multiple substitution models until it ...
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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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2 votes
2 answers
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How can I improve or otherwise investigate an unreliable genome tree?

Summary My genome tree doesn't agree with my gene trees and I get the feeling that my genome tree might be wrong, possibly due to long branch attraction, but I don't know how to check/fix it. ...
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Generate consensus protein sequence from relatively gappy alignment?

I would like to know what would be the best way to generate a full-length consensus sequence? I want to obtain a single representative sequence from a relatively gappy multiple sequence alignment of ...
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2 votes
1 answer
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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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Extract SNPs from multiple sequence alignment

I’m wondering if folks have recommendations for tools/scripts to extract SNP sites from a multiple sequence alignment of consensus bacterial genomes? Specifically, I am interested in a multiple ...
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1 vote
2 answers
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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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3 votes
1 answer
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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
1 vote
1 answer
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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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2 votes
1 answer
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Biopython reads my tree eternally long

I have a nexus tree (1332 taxa) with a lot of additional data. When I tried to read it through tree = Phylo.read(treepath, "nexus"), my kernel got ...
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3 votes
1 answer
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What is & how to solve File error: my.xml.state (Remote I/O error)?

I caught the next exception during my phylogeographical analysis in BEAST 2 with GEO_SPHERE. What could be the reason? & how to evade this in the future? ...
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  • 355
3 votes
1 answer
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Tree Building Algorithm that treats gaps as deletions

I'm part of a nanopore sequencing experiment that will sequence several generations of viruses. The intent is to perform directed evolution by putting selective pressure on these viruses and tracking ...
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3 votes
2 answers
95 views

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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  • 355
3 votes
1 answer
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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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  • 355
2 votes
1 answer
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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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0 votes
1 answer
100 views

BEAGLE do not see and/or not use OpenCL

I am conducting phylogeny analyses using BEAST 2 as software tool. It is said that it can be accelerated by BEAGLE-library. I have a personal laptop with Windows & a cluster with CentOS. I ...
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  • 355
-1 votes
2 answers
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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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  • 355
2 votes
1 answer
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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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3 votes
2 answers
351 views

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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2 votes
1 answer
32 views

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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1 vote
2 answers
76 views

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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2 votes
1 answer
44 views

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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  • 121
3 votes
2 answers
84 views

How to get the number of complete phage genomes available on ncbi?

I am looking to establish the total number of complete phage genomes available on NCBI. I am not looking for any specific type, but want to understand the total diversity available. How can I perform ...
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1 vote
2 answers
41 views

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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1 vote
2 answers
88 views

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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1 vote
2 answers
45 views

Remove variable sequence component within a tree text file

I have a gene tree file of 436 orthologue genes from 6 species. I want to remove unwanted extensions as it looks massy after visualization. My file looks like: (TRINITY_Clupea_DN5452_c0_g1_i1.p1:0....
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3 votes
2 answers
94 views

Correspondance of SARS-CoV-2 annotations (Nextclade - Pangolin)

Is there any annotation file providing correspondence between Nextclade and Pangolin variant nomenclature/annotations, to annotate some SARS-CoV-2 genomes from Gisaid with both these? For the moment I ...
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2 votes
1 answer
59 views

At what point is a gene different between species that we call it a different gene?

I am new to genetics and I know humans share many genes with mice for instance but that there are slight differences in conserved nucleotide sequences. Is there a community consensus around at what ...
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1 vote
0 answers
27 views

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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2 votes
1 answer
17 views

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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0 votes
1 answer
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How to identify Father-Daughter Relationship from Phylogenetic analysis?

I have performed a phylogenetic analysis using CLUSTALW and obtained a phylogenetic tree. I know how to read a phylogenetic tree and how to relate the sequence similarity between two sequences by ...
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0 votes
0 answers
37 views

Selection analysis based on each leaves as foreground with FastCodeML

I have to test the selection for each leaves in a phylogenetic tree. In normal case(with codeml), I will be running model zero for all leaves and then model 2 for each leaves as foreground (marking ...
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5 votes
1 answer
49 views

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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0 votes
0 answers
38 views

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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4 votes
0 answers
62 views

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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1 vote
2 answers
31 views

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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0 votes
0 answers
48 views

Difference in BLAST and eggNOG

Note: this question has also been asked on Biostars This is question regarding the tools rather than the concepts. I am a freshman at college and I am a working on an evolutionary biology of ...
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3 votes
2 answers
122 views

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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1 vote
0 answers
12 views

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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0 votes
0 answers
12 views

How to run a phylogenetic analysis with non-independent data?

These are the facts: I am working with some morphological features. Each trait can have one of the following three states: 0, 1, 2. State 0 is always independent. But if there is a trait with state 1, ...
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2 votes
1 answer
55 views

Can ortholog genes have different names among different species?

To be specific, we have different lineages of E. coli. I wondered if the ortholog genes among them should all have the same name in all lineages or can they also have different names?
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1 vote
0 answers
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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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0 votes
0 answers
28 views

How is the instantaneous rate of an instantaneous rate matrix determined?

In molecular evolution, I know that the instantaneous rate of the rate matrix is the limit of the rate as time approaches 0, but what I don't understand is how this rate is established or what I can ...
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0 votes
0 answers
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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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  • 81
2 votes
1 answer
49 views

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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2 votes
2 answers
78 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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0 votes
1 answer
30 views

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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  • 149
2 votes
1 answer
51 views

Fitting branch models with godon

Is it possible to fit branch models (Yang and Nielsen, 1998) in godon? That is, the model which averages over all sites, as opposed to the branch site models?
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