Does the phylogenetic tree making tool IQTREE use evolutionary placement algorithm?

For my master thesis I am conducting a phylogenetic research and for this I'm using tools like MEGA, IQTREE, FigTree, etc to make a phylogenetic tree. I wanted to know if IQTREE integrates the...

14 February 2021 1,541 2 View

Is there an alternative to PGLS that considers phylogenetic signal when calculating the estimated value?

I have been working on a study trying to estimate body mass in mammals using a skeletal proxy in R. My dataset has high phylogenetic signal (Pagel's Lambda = 0.9) and I am interested in removing...

26 January 2021 6,997 3 View

Question regarding investigation of the nature of bacteria: whether it can cause human diseases or not?

Hi all, Considering that one has the whole genome sequence (annotated) of a bacterium and wants to know if it has the potential to cause human diseases, what steps would you recommend...

26 January 2021 8,732 3 View

Are phylogenetic independent contrasts still used in biology?

I have a regression equation in which I am curious if the amount of scatter around the regression line is driven by phylogeny. I know there is a lot of phylogenetic signal because Pascal's lambda...

22 December 2020 937 1 View

Why am I getting inconsistent results from my ChIP PCR?

One of the times I performed this ChIP I got strong binding at the locus I amplified, but I have not been able to reproduce this result after many many tries. However, I did get the protein I am...

10 December 2020 7,279 1 View

Could anybody provide insights the best tools to create a custom database for taxonomy assignment of metagenomic data?

I am interested in the different tools that can be used to create custom databases for targeted sequencing and how to trim the databases based on the amplicon size? Also, should custom databases...

02 December 2020 3,105 3 View

EDGAR - How to add Whole genome sequence of the strain (novel) to EDGAR comparative genomic tool for comparison?

Hi all, I am interested to do a comparative genome analysis using EDGAR comparitive genomic tool. I have a novel bacteria whose genome sequence was obtained by us and now I was to do compare this...

10 November 2020 3,489 3 View

Field emission simulation using PIC method, how to inject particles properly?

I am trying to implement PIC-code for the field emission simulation. According to PIC loop particles injected after calculation of charge density. But I stuck at the problem that at some points of...

01 November 2020 3,446 1 View

Which methods (or modern programms) are used to assess the biodiversity of highest vascular plants?

27 October 2020 240 3 View

R package for GLMM with phylogeny (but not for community composition)?

Hello, I have a dataset derived from a multi-species experiment that I carried out. I have 30 different plant species from several families and 3 geographical groups. I applied 6 different...

26 October 2020 874 3 View