Biology Stack Exchange
Biology Stack Exchange

Questions tagged [phylogenetics]

A sub-discipline of evolutionary biology which involves the study of evolutionary relatedness between different organisms based on their molecular and morphological features.

A sub-discipline of evolutionary biology which involves the study of evolutionary relatedness between different organisms based on their molecular and morphological features.

219 questions
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Branch length in phylogenetic trees

I know this is a very basic question, but it is not too clear to me what is the unit of measure of branch length in phylogenetic trees. I have come to understand that it is usually expressed in number of substitutions/site/some unit of time. What is…
Beatrice Baldi
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How can I tell if a certain marker is useful to date a phylogeny?

If I have a phylogenetic tree for a genus, how can I tell if a certain protein would be a good phylogenetic marker to use if one wanted to use a molecular clock to date the age of some speciation event in that a genus? How can I look for it on a…
Bakhtawar
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What does the hominin phylogenetic tree look like?

I'm no biologist, but I'm curious what the rough phylogenetic tree looks like for Hominin. Could you create a rough sketch that includes: Homo rudolfensis Homo ergaster H. georgicus H. antecessor H. cepranensis H. rhodesiensis Homo…
RubeOnRails
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DNA barcoding, querry regarding tree based (cluster) methods for species identification

I am working on success rate of DNA barcoding in identification of species using distance and tree based methods. Regarding distance based method, I have used Adhoc and species identifier and confirmed species identification using best closest…
Rahul
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The protostome/deuterostome distinction and why it is important

As I unerstand it, at some point an embryo develops a hole; this hole continues to punch through, and eventually makes an opening at the other side of the embryo. If the original hole becomes the mouth, then the organism is called a protostome. If…
Ovi
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How to interpret weighted Robinson-Foulds distance between phylogenies?

The Robinson-Foulds (RF) metric provides symmetric distance between two phylogenies as a sum of monophyletic groups present in one tree but not in the other. The normalised RF distance is given as $\frac{RF_i}{RF_{max}}$. Let's consider an…
nya
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Metazoan branching: Placozoa or Porifera?

Of Placozoa and Porifera, which branched off first? (Conversely: which are closer cousins to us?) I've heard both suggested as our most distant cousins with bodies, so was wondering which ordering is currently considered most likely. Of suggestions…
Bertie Wheen
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How do I generate a phylometric tree given species names?

I have a list of species. I want to put those names into a tool and get back a visualized tree that includes names of shared order, suborder, family and genus. Is there an existing tool that does this job for me or do I need to program my own…
Christian
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phylogenetic Independent contrasts with unresolved tree

I have a dataset containing morphological and performance measures of species from various groups, including insects, lizards, frogs, spiders etc, and want to analyse the relationship between these measures and the animal's body size via regression…
Peter
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Blood samples in cell lysis

I will be joining a team of field biologists on a trip to some uninhabited islands in the tropics. We will be collecting bird blood samples for some genetic research. We will be out there for two weeks. Will blood samples in lysis buffer last for…
Dacia Wiitala
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How to get the file of a published phylogeny of a taxon

If an article has a published phylogeny, is it common to get the newick file with branch lengths from the authors? In order to do further research with the tree.
Ferroao
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Finding different Proteins with same function

Could you help me about finding two different proteins that coming from different ancestors, perform same function? Thank you
Ali G
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How to use a published phylogenetic tree?

I would like to know how should I use a phylogenetic tree from an already published article, to put it on my own article so I can analyze the evolution of a trait. Is there any software I can use, or do I only have to "edit" the tree with a…
Diego Lopez Spahr
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Infer distance since duplication from tree?

Question I have a really simple question, but I'm not able to figure it out. I made a tree (using BLOSUM62). Here is a part of the tree: How can I calculate the distance till the duplication event occured between HBD en HBB? just for HBB 36.21…
KingBoomie
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Calculating ultrametric distance matrix

I am fairly new to phylogenetic analysis, so I'm guessing this is a basic question. If I have a bunch of aligned sequences, and I ultimately only care about pairwise distance (e.g. for calculating phylogenetic diversity) then is there any way to…
user3037237
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