Which algorithm is better to generate a phylogenetic tree?why?

02 October 2018 1 9K Report

Hi,

I am using the software PyElph to investigate the similarities between RAPD profiles of a few bacterial isolates. My question is: Which algorithm is it better to use to generate the phylogenetic tree? UPGMA, Neighbor Joining, WPGMA, Single linkage or complete linkage?And can you explain me why?A lot of papers mention UPGMA for the generation of dendrograms to study the relationships between bacterial isolates, but I can't find why.

Thank you very much in advance.

Silvia

Silvia Caprari

I forgot to say that the isolates belong to the same bacterial species..i don't know if it is relevant

Badges
Science topic

More Silvia Caprari's questions See All

I am working on my Master's thesis on the biogeography of the genus Ruagea and I would like to ask, could someone help me to check whether my result?

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...

28 July 2024 2,979 1 View

What could be plastic adherent cells from PBMCs maintained in High Glucose DMEM 15% FBS ?

I'm trying to obtain MSCs from whole blood PBMCs and from the CD34- fraction of umbilical cord blood. However, I'm obtaining other types of cells that prevent the MSCs from growing. These cells...

26 June 2024 3,664 1 View

Hemodialysis technician professional profile ?

What is the hemodialysis technician profile and the relationship to hemodialysis nurse, have you got experience about this or have you a technician among your staff?

01 May 2024 3,635 0 View

How to use AI in architecture design process?

29 January 2024 1,792 4 View

Does anyone know if there is any protocol for measuring the concentration of bile salts without using the kit proposed by INFOGEST?

28 November 2023 3,334 0 View

What is the approximate concentration of bile salts after measuring with the kit proposed by INFOGEST?

28 November 2023 8,122 0 View

What is the limit pass of T24 and RT4 bladder cell lines?

Can anyone tell me what is the maximum pass of T24 and RT4 bladder cell lines? Thanks

10 October 2023 2,978 0 View

What is the doubling time of T24 and RT4 bladder cell lines?

Can someone confirm that the doubling time for the T24 cell line is 19 hours? This is the information provided to me by the commercial house where we have purchased. (Cell Lines Service) And for...

10 October 2023 2,412 1 View

How is cryopreservation T24 and RT4 bladder cell lines?

Could someone tell me the freezing medium you use to freeze the RT4 and T24 bladder cells? I found on Elabscience (www.elabscience.com) that for T4 it is: 60% basal medium+30% FBS+10% DMSO. For...

10 October 2023 9,474 0 View

Have you ever used the ROUT method to find the outliers of a single variable instead of those of a non-linear model?

This method for finding outliers when fitting data in a non-linear regression model is explained in the following article. Detecting Outliers When Fitting Data With Nonlinear Regressi......

26 March 2023 2,529 0 View

Why doesn't Average standard deviation of split frequencies change in phylogenetic analysis?

I've run it three times to try different parameters, but it stops changing after running for a short while. Please help me understand how to fix this. Is there a problem with the sequence or the...

15 May 2024 5,536 1 View

How to deal with zero/negative growth rates in tree growth models?

Tree growth is an important aspect of forestry and forest ecology. Typically a growth rate is calculated as the difference between two stem diameter measurements over a given time interval: (dbh2...

15 May 2024 8,739 2 View

What criteria define a tree species as monodominant within a given ecosystem?

I am looking for criteria to define a species as monodominant, based on its DBH and presence locations in the field.

13 May 2024 7,716 3 View

I have DNA sequences of ITS1 genes both forward and Reverse sequences. How do i build combined phylogenetic tree from these?

None

10 May 2024 5,322 2 View

Which is the best free software for RAPD data analysis?

I am searching for a free best software for RAPD data analysis and phylogenetic tree construction

09 May 2024 7,017 3 View

What cut off values should I use for my phylogenetic tree?

Hi, I am currently constructing a phylogenetic tree involving heterokonts, specifically of marine diatoms and dinoflagellates. Looking at the BLASTn results of my query sequence, I am wondering...

30 April 2024 4,239 2 View

How could a phylogenetic tree be constructed from plant biological name within the Family, or, from distant family??

Can I make a phylogenetic tree from multiple plant biological name within the family, or, from distant family? Thanks in advance.

06 April 2024 5,496 3 View

What are exactly the different types of fetomaternal interdigitations in placentas?

I am quite confused because some sources distinguish between 5 types: folded, lamellar, villous, trabecular, labyrinthine (e.g. Benirschke's Pathology of the Human Placenta ; Evolution of the...

13 March 2024 7,798 2 View

Multilocus phylogenetic analysis or core genome phylogeny. I need help. ?

Guys, I need help with phylogeny. I am very new to this field and currently trying to position a bacterial strain. I have selected four crucial loci for the genus, but I am encountering...

02 March 2024 6,182 3 View

How much of the weight of tree of heaven (Ailanthus altissima) contains of water?

Dear researchers, I need to know that how much of the dry and green weight of the tree of heaven (Ailanthus altissima) may contain water? Is there a reference on that? Thank you for your...

27 February 2024 1,959 5 View