07 April 2025 4 10K Report

Hi all!

I want to construct a phylogenetic tree of all earthworm (Lumbricidae) COI sequences available on GenBank.

My search on the NCBI nucleotide database has retrieved about 10,000 sequences. Obviously, I can't construct a tree using all these. Also, I realize there will be redundant results, duplicates, and unverified sequences.

What would be my next step when dealing with these sequences? Should I clean my dataset of 10,000 sequences? If yes, how would I do that? Which tools or software are commonly recommended?

Any insight on the logical next steps would be immensely appreciated.

More Kamyar Amirhosseini's questions See All
How to maintain soil moisture level at field capacity in a pot experiment?

I have been boggled by a seemingly simple problem. Many studies state that "The water contents of the pots were checked daily by weighing and adjusted to field capacity." How is this performed?...

08 June 2024 5,207 8 View

To which taxonomic levels do different approaches allow for prokaryotic identification?

I need to know to which taxonomic levels (from phylum to species) the following approaches allow prokaryote identification: a) morphology-based approaches b) chemotaxonomy c) GC content d)...

23 January 2024 4,523 6 View

How to prepare soil samples for microplastics exposure treatments?

In research where the objective is to study the impact of microplastics on soil properties, is it necessary to evaluate the original microplastic concentration of the test soils? If the soils...

27 November 2023 248 8 View

What biofilm carriers are commonly made of?

I am planning to cultivate algae-bacteria biofilms under greenhouse conditions using biofilm carriers. I have routinely come across Industrial Soft Carriers as frequently used substrates for...

06 June 2023 2,897 1 View

What percentage of library matches are generally acceptable in microplastics analysis?

I recently ran an FTIR analysis to identify two unknown microplastics. The result indicates a matching percentage of over 50% with polyethylene for both particles. However, I wonder if these...

14 May 2022 1,588 5 View

Could the origin or source of microplastics be determined by their physical characteristics or shape?

This might be a long shot, but a while ago I read an article that provided detailed information on how the physical characteristics of microplastics (more precisely, the shape of particles) could...

27 March 2022 10,044 5 View

Will microplastics extraction be compromised if depth filters are used instead of surface (membrane) filters?

Normal Ashless quantitive filter papers from CHMLAB are readily available for me to purchase. However, I understand that using depth filters may compromise microplastics extraction processes as...

24 December 2021 3,580 5 View

How to calculate the amount (in grams) of NaCl required for 600 ml of saturated salt solution with density 1.2 g/cm3 ?

Any help is appreciated.

12 November 2021 516 11 View

How does stability of organic acids differ in most soils?

I recently read in a review article that oxalate is the most stable organic acid in calcareous soil which is due to the formation of ca-oxalate reducing its biodegradability. does this notion hold...

28 December 2020 6,212 3 View

Why does MgCl2 solution displays less conductivity than NaCl at constant ionic strength ?

This question is related to the application of EC in estimating the Ionic strength of a solution. But I have difficulties interpreting the difference between MgCl2 and NaCl curve. Any help is...

14 December 2020 5,867 3 View

Similar questions and discussions
How to learn more about SPSS and its Application?

I would like to learn more about SPSS and Its application especially in regards to data analysis. Please suggest me how I can learn more about it. Thank you so much.

11 August 2024 9,101 4 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

Baseline drift in HPLC? What causes this?

Hello, Why do i see this baseline drift when i compare my blank (black) to the sample (blue)? Any suggestions as to why this happened? Thank you!

11 August 2024 3,770 4 View

Text-Communication from the M1 Hand Area using BCI—and then there is Elon Musk?

Willett, Shenoy et al. (2021) have developed a brain computer interface (BCI) that used neural signal collected from the hand area of the motor cortex (area M1) of a paralyzed patient. The...

10 August 2024 7,180 0 View

Has anyone applied Python in the field of textile engineering for data analysis, automation, or smart textiles?

I'm currently exploring the application of Python in textile engineering, specifically in areas like data analysis, process automation, and the development of smart textiles. I'm interested in...

10 August 2024 7,429 2 View

How can I use the cif data obtained from rietveld refinement extracted via gsas2, for microstructural analysis using ETEX software?

How can I use the cif data obtained from rietveld refinement extracted via gsas2, for microstructural analysis using ETEX software?

09 August 2024 7,718 0 View

I can't see the ssDNA band after performing asymmetric PCR. Is there any way to do this?

After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...

08 August 2024 1,668 3 View

Does crude extraction using NaOH and Tris work well with Fungi?

I'm trying to find a DNA extraction method for fungi that does not require equipment and heating. Is there anyone who can suggest an alternative option? Thank you

08 August 2024 4,733 2 View

How are iso-frequency contours plotted?

Let's say we have a standard, regular hexagonal honeycomb with a 3-arm primitive unit cell (something like the figure attached; the figure is only representative and not drawn to scale). The...

07 August 2024 1,937 1 View

How to prepare the nanoparticle treated fungal sample for Environmental SEM analysis?

A fungal strain was treated with nanoparticles. We want to do an environmental SEM analysis. So could anyone share your views on preparing the sample? Thank you.

07 August 2024 5,307 1 View

Our partners will collect data and use cookies for ad personalization and measurement. Learn how we and our ad partner Google, collect and use data. Agree & close