Any advice on two-step PCR library generation with respect to Taq polymerase and 3' A-overhangs?

Hello! I am trying to sequence (Miseq) a custom amplicon from many samples using the Nextera indexes. For those of you not familiar, this involves a two step PCR protocol. The first round of PCR...

31 December 2014 6,211 6 View

Is there a tool available to remove sequences from a protein alignment based on conserved residues?

09 October 2014 4,157 9 View

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

Where Can I Get Hourly Wind Speed Data at 50 Meters Height?

Hi, I want to get three years of hourly wind speed data at 50 meters height for specific locations in Turkey. Unfortunately, I couldn't find any good websites for this. Do you know any online...

12 December 2020 323 10 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

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

How can I perform pairwise protein alignments using BLAST, but without search?

I have a set of about 1000 homologous protein sequences with high diversity across various genera and families. What I need is to perform BLAST alignment of each possible sequence pair and obtain...

25 October 2020 1,199 5 View