How can I enlarge "clade" in phylogenetic tree?

Jeong Hojun @Jeong-Hojun

22 October 2022 1 5K Report

Hello

I have to enlarge divergence point in phylogenetic tree.

because It is difficult to identify the node because there are few mutations and it is too close.

(Black dots are nodes)

Tyler Chafin

What are you using to plot with? You need to plot your tree as a cladogram rather than a phylogram. Both Dendroscope and Figtree have options for this (either explicitly setting plot type as cladogram, or something like "use equal branch lengths"), or if plotting in R using ape:::plot.phylo you can set use_edge_length=FALSE

Badges
Science method

More Jeong Hojun's questions See All

Any gel-type materials can be used for impedance matching?

Hi. I am recently designing biomedical antennas. The problem is the permittivity difference between the skin and the air is too big, so I am having difficulties in delivering RF power to the...

22 October 2020 6,833 5 View

Stephen Crothers Refutation of the Existence of Black Hole?

Why is nobody talking about Stephen Crothers mathematical refutation of the existence of Black Hole from his study of general relativity? He has been very vocal giving presentation at a conference.

11 October 2020 5,260 8 View

Symmetrical form of Maxwell's equation explains Light propagation in empty space and Quantum Mechanical uncertainty at the same time?

In physics, normally a critical information solves many seemingly unrelated problems at the same time. I think this is the case with the information that neutrinos are magnetic monopoles of...

11 September 2020 7,840 22 View

How can you remove reduced graphene oxide?

I am using a SiO2 wafer with gold electrode on top of it, and I'm looking for a way to "re-use" the gold electrode if possible. Is there a way to not hurt the gold electrode (that is very thin)...

15 June 2020 8,300 4 View

What is wrong with my ligation and transformation of plasmid DNA?

Hi I am just an ordinary university student that is currently studying in a lab to graduate. I have not been long since I have been studying in the lab. Now I am learning how to make a vector and...

11 March 2020 2,277 3 View

Using GAN-generated faces to train face recognition?

As an undergraduate research project, I am thinking about training face recognition system using GAN-generated face data, instead of data generated by humans. I want to find out whether...

01 March 2020 7,062 3 View

Why potential window becomes shorter in Galvanostatic Charge Discharge (GCD) compared to Cycling Voltammetry (CV)?

I use iviumsoft for CV and GCD in order to measure electrochemical properties of supercapacitor electrode material. Let's say that CV curves make pretty large shape in potential window of 0 to...

05 April 2019 4,520 6 View

How do I minimize exposure to room air just after exposure to hypoxia?

I am planning an lab study on effect of hypoxia on glucose metabolism of cancer cell. For hypoxia exposure, I am considering anaerobic chamber system. My concern is that if I use this chamber,...

14 March 2019 7,641 8 View

In supercapacitor, how can certain materials are used for certain electrode material?

transition metal such as Mn, Ni, Co, Cu etc are more likely used as positive electrode whereas some others such as Bi, Fe, Mo, Carbon etc are more likely used as negative electrode materials....

28 February 2019 2,886 2 View

Why are side chain lengths different by 4 like hexyldecyl(HD), octyldodecyl(OD). Why don't we use symmetric side chain?

why are all side chain lengths different by 4 like hexyldecyl(HD), octyldodecyl(OD), decyltetradecyl(DT). Why don't we use symmetric side chain? I appreciate any references that show the different...

27 February 2019 4,078 1 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View