Where to find data on trees in tropical agroforestry?

Hi, I'm looking for data (mainly related to management: growth rate, canopy size, soil and climate preferences, etc.) about tropical trees used in tropical agroforestry. Have you ever heard about...

28 February 2021 7,356 8 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

When making a phylogenetic tree, do I need to concatenate the chromosome and the plasmids for my reference?

This is such a basic question but I come from a non-bioinfo group so I keep getting different answers. I was wondering if when making a phylogenetic tree whether you have to concatenate the...

14 January 2021 2,492 2 View

How can I build one phylogenetic tree for an arthropod community when I had known their scientific names?

I am working on the phylogenetic analysis for communities of plants and arthropods. A standardized protocol of building phylogenetic tree for plant species list that was widely used in studies....

29 December 2020 181 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

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

How can I get Genbank accession code given the scientific names?

Hello! I now have a complete list of about 23k plant species that I want to check if Genbank has the sequencing data for a phylogenetic analysis later, and I am really new to the topic. Is...

02 November 2020 4,450 3 View

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

27 October 2020 240 3 View