Questions tagged [phylogeny]

Phylogeny is a statistical approach for reconstructing evolutionary relationships using trees

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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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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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1answer
59 views

Can't load files into PopART

I am trying to create haplotype networks in PopART which I have successfully done many times in the past. 2 weeks ago the program was working fine for me but recently I am unable to load files. What ...
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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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1answer
40 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: 1 ) A phylogenetic tree in newick format : <...
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35 views

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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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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85 views

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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1answer
132 views

How many single copy gene are needed to construct the phylogenetic tree?

I ran the orthomcl program with genomes of the whole streptomyces genus(from ncbi) as input, but I only got 22 orthologous groups(streptomyces's genome size vary from 2M to 15M, which shows the great ...
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35 views

Algorithmic Information Measurement of Human Genome Databases?

What is the highest data compression ratio achieved on a population of genomes measured to include the compressing algorithm itself? The size of the compressed database approximates its algorithmic ...
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187 views

Calculating the trimming parameter when constructing an additive phylogeny

How do you calculate the trimming parameter when constructing an additive phylogeny? I think it has a relationship with the length of the shortest hanging edge, but I can't figure out how this works.
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45 views

Confusion related to effective population size

I am making a demographic model for African American population in which I say 80% of ancestry comes from African population and 20% comes from European population. I am using the time/population time ...
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1answer
273 views

What do negative dN or dS mean in cal_dn_ds in Biopython?

I'm noobie in bioinformatics. I use cal_dn_ds from Bio.codonalign.codonseq with method 'NG86'. Sometimes I get dS=-1. What does ...
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390 views

How to create a dendrogram of clusters and reconstruct phylogenetic relationship

I'm working with a Daphnia data set looking at the 16s gene pulled from the BOLD database. So far I did a multiple sequence alignment and attempted to cluster and plot a dendrogram: ...
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56 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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81 views

efetch nucleotide -> protein ids

I'm downloading translated viral genomes initially via Blast - which had shortcomings - and now by efetch. What I want to do is obtain a complete list of all ...
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1answer
86 views

How can i get data set of illness and not illness people?

I'm reading a virology paper where the authors made a classification for the patients as to whether they had a specific disease outcome or not against the underlying sequence ... The research focused ...
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1answer
69 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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1answer
228 views

Can I use BioEdit to quantify the sequence similarity?

I am using BioEdit. It can perform an align of multiple sequences. Can this sequence similarity be outputted as a value, e.g. 70%?
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1answer
42 views

After KEGG and GO analysis, how to make tables+phylogenetic trees

hope everyone is ok. I used Trinity to do a de novo transcriptome assembly, then blastp/blastx and then used Blast2GO software to do KEGG and GO analysis. So i got some txt files with header : for GO ...
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1answer
40 views

Phylogenetics analysis between diverse species

Hope everyone is well. So i was appointed with a task, and i need some guidance. Attention, the one that gave me the task may not have explained this very clearly. I will write what he exactly asked ...
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1answer
56 views

Relationship between the instantaneous rate of change of a continuous time Markov model and the rate of a global clock model?

If continuous-time Markov models contain a parameter q that denotes the instantaneous rate of change and a global/strict clock model is the overall rate of evolution, how are these two parameters ...
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1answer
710 views

How to generate ultrametric phylogenetic trees?

This question has also been asked on Biostars I am going to use ultrametric tree for downstream analysis. I would like to see use the ultrametric tree for Ranger-DTL for infer gene family evolution by ...
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2answers
77 views

Why does `pratchet()` in `phangorn` not find the most parsimonious trees?

I called pratchet() on a dataset with binary values for the characters and it returned a parsimony value of 35. I then calculated the parsimony value for the ...
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37 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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42 views

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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1answer
29 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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Can we use reference strain as an out-group strain to root SNP based species tree?

I have generated a species tree based on whole-genome SNP using CSI_SNP_Phylogeny, wherein I used Reference strain as an outgroup to root my species tree (SNP fasta were downloaded and RaxML used to ...
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2answers
115 views

Inferring a phylogenetic tree from BLASTn

I am trying to infer a phylogenetic tree from a Blastn output and from what I have understood, what I should do is 1) extract the alignments and re-align them using Muscle, then 2) feed the .aln file ...
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149 views

Algorithmic investigation of viral proteins for vaccine design [closed]

I wish to investigate how a virus could be attenuated through targeted mutagenesis by a priori prediction of attenuating amino acid mutations. In particular, I am seeking bioinformatic solutions where ...

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