Filippo Nicolini

Filippo Nicolini

Reasearch Associate dealing (struggling) with invertebrate evolutionary genomics.

Resources

Last updated: Oct 27, 2025

Here you can find a series of tools, materials, and creative works I have been developing throughout my research and outreach activities. Feel free to get in touch for anything you’d like to discuss!

Introduction to bioinformatics

In my GitHub personal page you can find a brief introduction to bioinformatics. There, I explain the most common bash commands that bioinformaticians usually deal with.

Take it as a friendly resource for accessing commonly used commands in early bioinformatics.

bash github tutorial

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phySCO: phylogenomics from Single-Copy Orthologs

Tired of tedious phylogenetic pipelines to generate species trees after a successful BUSCO analysis? Fed up with wasting time copying and pasting commands to align, trim sequences, and infer trees?

Here's the solution! Let phySCO transform your workflow today!

phySCO is an all-in-one python tool that (i) takes the output of a series of BUSCO analysis, (ii) retrieve ubiquitous single-copy BUSCO orthologs, (iii) align and trim them, and then (iv) infer the corresponding ML phylogenetic tree using a partitioned analysis. Enjoy it!

phySCO

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Wet-lab protocols

Researchers always complain—rightly—that bioinformatic code is not always shared and that analyses are rarely fully reproducible.

But have you ever thought about wet-lab protocols? How many times have you tried to run an experiment for the first time, only to find yourself piecing together details from five different papers just to create a first draft?

Just like bioinformatic pipelines, wet-lab protocols should be openly shared and easy to access. That's why I decided to start documenting my protocols on GitHub, where anyone can use them and also browse previous versions.

Wet-lab protocols

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Illustration portfolio

In my free-time I also like drawing. And sometimes I try to merge this hobby with my research work and get illustrations to use on papers and/or other publications.

Feel free to get in touch if you may need something of this kind.
  • Animal icons. These have been used to decorate phylogenetic trees, plots and other paper figures. Up to now, I've mostly focused on organisms that I personally study (i.e., branchiopods and bivalves).

animal silhouettes

  • Sex determination. These are random images I drew to put in my presentations about the (confusing) sex determination of bivalves.

sex determination

  • Insect developmental biology. These have been used in the chapter "Hexapods: reproductive biology and life cycles" ("Esapodi: biologia riproduttiva e cicli vitali"), edited by Barbara Mantovani, Liliana Milani and Rialdo Nicoli Aldini, from the book "Systematics and evolution of hexapods" ("Sistematica ed evoluzione degli esapodi"), edited by Alessandro Minelli e Marco A. Bologna, Liguori Editori (2023). All rights reserved.

insect development

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Poster collection

Here you can find the pdfs of posters where I was involved in first person. Posters that I personally presented are indicated by a DNA symbol. Click on the titles to see the full posters and download them!

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Grant and funding applications

The survivorship bias is the tendency to draw conclusions only on the basis of those who survived, while overlooking those who didn't. As one great professor once taught me, this bias is particularly strong in evolutionary biology, and we should always be aware of its existance.

But the survivorship bias is more widespread than we think, and academic careers are no exception. Behind successfull researchers and research lines, there are always (always) grant applications and experiments that didn't succeed.

Therefore, also inspired by some collegues, I started gathering below all the grant, award, scholarship, and whatever applications I made—no matter their outcome. Maybe this can be helpful and encouraging to others.

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