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Questions tagged [phylogenetics]

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

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Are phylogenetic tree construction algorithms any different than general clustering algorithms?

I suspect the answer is no. But I don't know enough to be sure that that is the case. Of course phylogenetic tree construction uses biological knowledge, e.g special distance metrics, but does it ...
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0answers
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How snippy makes MSA-like aligned fasta output from multiple samples?

From the log file it seems snippy doesn't do assembly. It only does mapping: fastq --> SAM --> BAM --> VCF --> consensus_seq/snps But if multiple ...
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1answer
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help interpreting my phylogenetic tree construction of bacterial species in same genus

I constructed a phylogenetic tree using mole blast and it created a neighbor joining tree so i used the alignment of those sequences with mine (1-43) in mega with TN93+G+I model but I dont understand ...
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25 views

Common Mouse and human DEG analysis

I have DEGs from human and mouse (equivalent of a human disease model), and would like to generate a logCPM correlation plot between the overlapping mouse and human gene (275 genes). Prior to ...
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3answers
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How to create Phylogenetic Trees from fasta files in Python or R?

Given around hundred fasta files with DNA sequences with good coverage, how could I create a Phylogenetic Tree from it? Ideally in python or R. I found Phylo from <...
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2answers
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Calculate the percentage of each unique phylogenetic tree in a BEAST output

I have a nexus formatted BEAST output containing 20,000 phylogenetic trees of seven taxa. Is there any way to get the percentage of each unique phylogenetic tree contained in this output? I already ...
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2answers
62 views

Perfect Phylogeny vs Maximum parsimony

I am searching various sources about phylogenetics. I saw some materials about perfect phylogeny and also phylogenies acquired from maximum parsimony constraint. They seem very similar to me. Are they ...
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2answers
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Truncating branch length values of Phylogenetic tree with biopython

I have been using biopython 1.72 to display my phylogenetic tree files. 1)Using the function 'Phylo.draw(pars_tree, branch_labels=lambda c: c.branch_length)' to ...
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1answer
44 views

How do I interpret the function O(f^-2 log n) in Shekhar et al. (2017)?

The results of Shekhar et al. (2017) "indicate that ASTRAL requires $\mathcal{O}(f^{-2} \log{n})$ gene trees to reconstruct the species tree correctly with high probability where n is the number of ...
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1answer
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MrBayes runs as single-core, but hangs when multi-core

I successfully compiled MrBayes v3.2.7 from github, with the configuration options ./configure --without-beagle --enable-mpi. The program is called mb. I tried one ...
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1answer
85 views

What is outliers and how to determine outliers in the following phylogenetic tree?

I confused with the term 'outlier' and 'outgroup'. Could someone explain with the example phylogenetic tree above? Thank you very much !!!
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1answer
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Does the “.full.aln” file produced by snippy-core contain all bases of my input sequences aligned to the reference genome?

I have a number of sequences and a reference genome. I used snippy to align each individual sequence with the reference genome. I then used ...
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1answer
64 views

How do I interpret my phylogenetic tree construction from Glucosidases in the Actinobacteria class?

Dear knowledgeable bioinformaticians, I'm currently pursuing an undergraduate degree and as a result I do not have so much knowledge in this topic. I'm having some troubles understanding my ...
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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: ...
4
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1answer
34 views

In calculating the retention index, why do we use the character state with the lowest frequency?

To calculate the retention index for a phylogenetic tree, we use the following formula: $$\frac{\text{maximum number of steps on tree - number of steps on the tree}} {\text{maximum number of steps on ...
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0answers
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Is there an R package that computes homoplasy excess ratios (HER)?

I want to calculate the homoplasy excess ratio for a phylogenetic tree and a dataset with character states and am wondering if there are any R packages out there that will do this.
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1answer
71 views

What is a site in a phylogenetic tree?

When I read about a term related to phylogenetics, for example, $K_a$/$K_s$ ratio, I constantly see the word site, whose meaning isn't explained and it puzzles me. Substitutions per synonymous site, ...
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76 views

How to plot character state changes from a presence-absence matrix on to a phylogeny

I am trying to assign character state changes from a presence-absence matrix to a phylogeny. I have tried assigning each character to its leaf node, and then if the leaf node's sister has the same ...
2
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1answer
49 views

Random addition method for phylogenetic tree reconstruction

I have been working on nucleotide/protein data files to reconstruct maximum parsimony trees. As I have used MEGA software to get parsimony tree, "random addition" method is used to generate initial ...
4
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1answer
68 views

python package for NNI neighbors

I am working on protein sequence data files for reconstructing phylogenetic tree and I need to generate all NNI-neighbours of the tree (two trees are NNI-neighbours if one can be transformed into ...
6
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1answer
82 views

Getting all NNI trees of a parsimony tree

I have an aligned protein sequence file which I have been using for reconstructing a parsimonious tree. I am currently using NNITreeSearcher._get_neighbors method from Biopython 1.72 but it's way to ...
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0answers
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How to make year scale bar unit in figtree software?

I have generated phylogenetic trees for virus sequences by using beast software. I observed in various research articles that the phylogentic trees also have a scale-bar (which mostly represents ...
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1answer
64 views

A basic question about phylogenetic inference with Bayes-MCMC

I am new to the world world of Bayesian-MCMC inference and have been working my way through various texts. I am having some difficulty understanding how MCMC works. I understand that it is a way of ...
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2answers
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Do any computational phylogenetic methods enable the specification of ancestral states?

Various phylogenetic algorithms estimate ancestral states of a phylogenetic dataset. Is there a way in either maximum parsimony, distance-based methods, or Bayesian inference to indicate what the ...
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2answers
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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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2answers
152 views

How do I estimate branch length of a maximum parsimony phylogeny in R?

I am trying to estimate a phylogenetic tree in R with ape and phangorn. With pratchet() and optim.parsimony(), I can estimate a ...
3
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1answer
140 views

Test to determine if two genes/exons share the same evolutionary histories?

In classic phylogenetic inference one is usually given various orthologue sequences of a given gene across various species. Those sequences are then multiple aligned and used to construct a ...
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1answer
83 views

Issues installing Dendropy

I want to perform phylogenetic analysis using Dendropy. I have installed dendropy using command sudo pip install -U dendropy but when I import it in python3.5.1 it ...
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1answer
118 views

Problems in creating desired phylogenetic tree with ggtree

I am working on haplogroup data and want to make a tree out of haplogroups using ggtree. I have following data in newick format. ...
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1answer
355 views

Biopython Phylogenetic Tree replace branch tip labels by sequence logos

Having recently constructed a lot of phylogenetic trees with the module TreeConstruction from Phylo package from Biopython, I've been asked to replace the branch tip labels by the corresponding ...
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1answer
113 views

How can I improve ESS values for ucldMean in beast?

Using starBeast I ran a 50 locus tree, with 34 individuals, using evolutionary models indicated by AICc in jModel test. I ran this tree with a MCMC chain length of 500 million, storing every 10,000 ...
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1answer
61 views

Combine multiple species trees

I have five species trees run using starBeast and Beauti. Here is a link to the paper discussing both, http://journals.plos.org/ploscompbiol/article/file?type=supplementary&id=info:doi/10.1371/...
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0answers
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State of the art mutation simulation software

There are many features affecting mutation probabilities, e.g. CpG mutations are 10-fold more likely than other types of mutations. Is there a model (preferably with software) which can take two ...
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1answer
114 views

Unable to Install PGDSpider using Ubuntu and wine

I'm running wine v 2.0.3 using ubuntu v. 16.04.2 on a Mac. I'm trying to install a program called PGDSpider2 from here. Essentially the program is supposed to convert different file formats used for ...
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2answers
110 views

Can we describe synthetic biological sequence data as belonging to a “species” or “taxon”?

For the purpose of testing phylogenetics software, we're using synthetic sequence data (i.e., it's computer generated, and there's no actual biological organism with that e.g. DNA sequence). For real-...
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4answers
1k views

How do I generate a color-coded tanglegram?

I want to compare two phylogenies and colour the association lines based on some metadata I have. I have been using ape cophyloplot but I have not had any success in getting the lines to colour ...
10
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1answer
325 views

What is the best method to estimate a phylogenetic tree from a large dataset of >1000 loci and >100 species

I have a large phylogenomic alignment of >1000 loci (each locus is ~1000bp), and >100 species. I have relatively little missing data (<10%). I want to estimate a maximum-likelihood phylogenetic ...