Address of the bookmark: https://github.com/martinjvickers/KAST

Address of the bookmark: https://github.com/sc932/ALE

To find repeats in a genome from 2 to 9 length using a Perl script, you can use the RepeatMasker tool with the "--length" option[0]. Here's a step-by-step guide:

Overview of SLiM and msprime

SLiM: Forward Genetic Simulator

SLiM is a free, open-source tool designed for forward genetic simulations. It allows researchers to model complex evolutionary scenarios, including selection, recombination, and demographic events, making it particularly useful for studying adaptation and selection in populations.

Key Features of SLiM:

• Simulates population evolution forward in time

• Supports custom evolutionary models using an embedded scripting language

• Allows modeling of spatial and ecological dynamics

• Provides high flexibility and extensibility for user-defined scenarios

• Available on GitHub as an open-source project

msprime: Ancestry and Mutation Simulator

msprime is an efficient, open-source tool that simulates ancestry and mutations using a coalescent framework. It is known for its high-speed performance and low memory requirements, making it a popular choice for large-scale genomic simulations.

Key Features of msprime:

• Implements coalescent simulations for ancestry modeling

• Efficiently simulates large population histories

• Supports the addition of mutations to genealogies

• Developed using an open-source community model

• Often faster and more memory-efficient than alternative simulators

Using SLiM and msprime with slendr

Both SLiM and msprime can be integrated with slendr, a framework that facilitates structured population genetic simulations. This integration allows for seamless comparison of simulation outputs.

How They Work Together:

• SLiM and msprime simulations can be analyzed within slendr.

• The ts_read() function in slendr enables loading and comparing tree sequence outputs from both simulators.

• This integration allows researchers to validate simulation results and gain deeper insights into evolutionary processes.

Performance Considerations

While SLiM offers powerful forward simulations with extensive customization, msprime is often preferred for its speed and memory efficiency when simulating ancestry and mutations. The choice between the two depends on the research goals:

• For detailed evolutionary modeling with selection and recombination: Use SLiM.

• For large-scale coalescent simulations with mutations: Use msprime.

• For comparing different simulation models and their outputs: Use slendr to integrate SLiM and msprime results.

Conclusion

SLiM and msprime are valuable tools for genome simulation, each serving distinct but complementary purposes in population genetics research. By leveraging the strengths of both simulators with slendr, researchers can conduct robust and efficient evolutionary simulations, enhancing our understanding of genetic diversity and adaptation.

For more information, check out the official GitHub repositories for SLiM and msprime, and explore the slendr framework for streamlined simulation workflow

However, pangenome graphs can be highly complex, making them difficult to visualize and interpret. A recent study published in BMC Bioinformatics introduces PG2 (PanGenoGrapher), an open-source, web-based tool designed to address this challenge. The source code and user guide are openly available on GitHub at https://github.com/iVis-at-Bilkent/pangenographer. A publicly accessible sample deployment is hosted at http://pg2.cs.bilkent.edu.tr. In addition, a demonstration video illustrating the primary use cases of PG2 is available at https://www.youtube.com/watch?v=yCd7-aGY6CQ.

PG2 combines advanced graph-layout algorithms with an interactive visualization platform. It allows researchers to explore genomic paths, identify variations, and examine relationships between different parts of a pangenome graph more easily.

This is important because visualization can play a major role in bioinformatics. When complex genomic information is presented clearly, researchers can more easily identify patterns, understand genetic variation, and generate new biological insights.

The development of PG2 represents a step toward making pangenome analysis more accessible and intuitive. As genomic datasets continue to grow and graph-based representations become more common, tools like PG2 can help researchers navigate this increasing complexity.

Ultimately, PG2 demonstrates how combining genomics, graph algorithms, and interactive visualization can make sophisticated biological data easier to understand and analyze.

Reference: Solun, G. K., Dogrusoz, U., Bingöl, Z., & Alkan, C. (2026). PG2: algorithms and a web-based tool for effective layout and visual analysis of pangenome graphs. BMC Bioinformatics. DOI: 10.1186/s12859-026-06555-4.

Scientists face a big challenge with the human genome. They can read its letters, but understanding their roles is much harder. Only about 2 percent of the genome codes for proteins. The rest acts like a huge control panel, deciding when and where genes turn on. With about 9 billion possible single-letter changes, testing them all in a lab just isn’t possible.

So, Google DeepMind asked a new question: what if we could predict what those changes might do?

This question led to the AlphaGenome Atlas (https://deepmind.google.com/science/alphagenome/atlas?), a detailed map of nearly every possible single-letter change in the human genome. Instead of checking each change one by one, researchers can use the Atlas to spot the ones most likely to matter. The AlphaGenome Variant Impact (AVI) score works like a trail marker, pointing scientists toward the changes worth a closer look.

This is where the Atlas gets especially useful. Much of the genome lies outside the protein-coding regions, where DNA acts as a switch or controller for genes. AlphaGenome lets researchers explore these areas and see how small changes could affect gene activity.

An atlas isn't the destination; it's a guide.

The AlphaGenome Atlas doesn’t replace experiments or solve every mystery. Instead, it helps scientists decide where to begin. From billions of possibilities, it turns the vast genetic landscape into something researchers can start to explore.

There are nine billion possibilities, a vast map, and maybe among them therWith nine billion possibilities and a huge map to explore, there may be clues hidden here to some of medicine’s toughest mysteries.

More at https://storage.googleapis.com/deepmind-media/DeepMind.com/Blog/alphagenome-atlas-a-predictive-map-of-every-possible-dna-letter-change-in-the-human-genome/alphagenome-atlas.pdf

A recent study published in Genome Biology (https://link.springer.com/article/10.1186/s13059-026-04280-y) addressed this challenge by introducing dicast (https://github.com/burgshrimps/dicast), a machine-learning approach for detecting structural variants in short-read sequencing data. Structural variants, such as large deletions, insertions, duplications, and inversions, can have significant biological and clinical implications, yet they are challenging to identify with short-read technologies. Because different detection methods frequently yield divergent results, researchers commonly employ consensus calling, considering a variant valid only if multiple tools detect it. While this approach reduces false positives, it relies on the potentially flawed assumption that the majority is always correct.

The researchers explored the impact of evaluating the supporting evidence for each variant, rather than simply tallying the number of algorithms that identified it. To establish a ground truth, they analyzed nine genomes using multiple sequencing technologies and 15 detection methods, initially identifying approximately 35 million potential variants. Through extensive filtering, evidence integration, and manual review of over 11,500 variants, they developed a robust benchmark comprising more than 236,000 structural variants. The findings underscored the complexity of the problem: short-read methods detected fewer than half of deletions and less than 10 percent of insertions, with performance declining markedly in repetitive genomic regions. In contrast, long-read technologies demonstrated superior detection capabilities. However, replacing the substantial volume of existing short-read data in clinical and research settings is not immediately feasible. Consequently, the researchers questioned whether short-read data might harbor more information than conventional analytical pipelines currently extract.

This line of inquiry led to the development of dicast. Rather than merely confirming agreement among multiple tools, dicast identifies patterns in sequencing data, including split and clipped reads, discordant read pairs, alignment characteristics, and the surrounding genomic context. An XGBoost machine-learning model evaluates which combinations of these signals are indicative of genuine structural variants. Thus, the approach shifts from tallying algorithmic consensus to interpreting the underlying evidence.

The researchers subsequently conducted a targeted evaluation by examining structural variants detected by only a single short-read tool, which are typically missed by consensus-based approaches. dicast successfully recovered approximately 81% of these single-caller deletions, insertions, and duplications. The signals for these variants were present in the data, but conventional filtering methods failed to integrate them effectively.

The utility of dicast was further demonstrated in cohorts with rare diseases, including congenital limb malformations, atrial fibrillation, and neuromuscular disorders. In one instance, dicast achieved a deletion recall rate of approximately 0.96, compared to 0.74 using consensus calling. The median number of variants requiring manual review was 29 per sample. Among 31 experimentally validated variants that standard filters would have missed, dicast identified 12, whereas consensus calling detected only one.

Overall, dicast identified approximately 20 percent more potential disease-causing deletions than consensus-based methods. While a 20 percent increase may appear modest, in clinical genomics such improvements can have significant practical implications. Missing a deletion may leave a case unresolved, whereas detecting a structural variant can provide critical diagnostic insights.

The study does not claim that machine learning has rendered short-read sequencing superior to long-read approaches. Instead, the results underscore the effectiveness of long-read sequencing for structural variant detection. However, dicast highlights a more nuanced perspective: substantial biological information may still be recoverable from the extensive short-read datasets already available.

The principal lesson extends beyond the detection of structural variants. For many years, bioinformatics pipelines have relied on threshold-based criteria, such as minimum coverage, quality scores, or support from multiple tools. While these rules are useful, biological phenomena do not always conform to rigid checklists; multiple weak signals, when considered collectively, can provide compelling evidence.

This perspective prompts consideration of the solitary variant: one algorithm identifies it, while several others do not. Traditional consensus techniques might have dismissed it, yet machine learning approaches evaluate the available evidence to determine whether the variant is plausible.

Occasionally, the most significant variant within a genome is the one that is almost universally overlooked.

Read more at https://link.springer.com/article/10.1186/s13059-026-04280-y

Research Area

Investigating the role in disease of both the microbe and its host (i.e immune system failure), using genomics and systems biology-based approaches
Using genomics and network analysis to characterize disease outbreaks and their environmental/social/genetic causes, and
Identifying new anti-infective and immune modulating therapies/biomarkers.

Link @ http://www.brinkman.mbb.sfu.ca/

The evolutionary connections between organisms are represented graphically through phylogenetic trees. Due to the fact that evolution takes place over long periods of time that cannot be observed directly, biologists must reconstruct phylogenies by inferring the evolutionary relationships among present-day organisms. 
Application of the techniques that make this possible can be seen in the very limited field of human genetics, such as the ever more popular use of genetic testing to determine a child's paternity, as well as the emergence of a new branch of criminal forensics focused on genetic evidence.
The effect on traditional scientific classification schemes in the biological sciences has been dramatic as well. Work that was once immensely labor- and materials-intensive can now be done quickly and easily, leading to yet another source of information becoming available for systematic and taxonomic appraisal. This particular kind of data has become so popular that taxonomical schemes based solely on molecular data may be encountered. Proponents even claim that taxonomy was previously based on morphology alone, which of course is utter fable.

For additional information on phylogenetics, see list of Phylogenetics Resources on the Internet.

Phylogeny and Reconstructing Phylogenetic Trees: http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html
the CBRG and Department of Statistics Phylogeny tutorial: http://www.compbio.ox.ac.uk/tutorials/phylogeny/
TUTORIAL: PHYLOGENETIC ANALYSIS USING PARSIMONY:http://home.cc.umanitoba.ca/~psgendb/GDE/phylogeny/parsimony/phylip.parsimony.html

PHYLIP: http://www.umanitoba.ca/afs/plant_science/psgendb/doc/Phylip/main.html
An Introduction to Molecular Phylogeny: http://bibiserv.techfak.uni-bielefeld.de/gcb04/tutorials/hoef-emden/GCB04Tut.pdf

How to make a phylogenetic tree: http://www.hiv.lanl.gov/content/sequence/TUTORIALS/TREE_TUTORIAL/Treetutorial.html
Phylogenetic Trees: http://cnx.org/content/m11052/latest/
Phylogeny by Ron Shamir: http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf
Introduction to Phylogeny: http://www.utm.edu/departments/cens/biology/rirwin/391/391Phylog.htm
Lecturer notes on Phylogeny: http://www.sbc.su.se/~bens/course_material/phylocourse1/lecture2.pdf
Principles and Practice of Phylogenetic Systematics:http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes.htm

Inferring phylogenetic trees: http://www.cis.hut.fi/Opinnot/T-61.6070/slides2008/pres_6070.pdf

Lecture Notes

Chapter 1 - The Diversity, Classification, and Evolution of Vertebrates:http://academic.emporia.edu/mooredwi/nathist/chap1.htm

Algorithms for Phylogenetic Reconstructions:http://lectures.molgen.mpg.de/Algorithmische_Bioinformatik_WS0405/phylogeny_script.pdf

Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. For more detail : http://www.phylogeny.fr/version2_cgi/index.cgi

A Brief Tutorial on Phylogenetics
http://bioss.ac.uk/~dirk/talks/tutorial_phylogenetics.pdf

A Brief Tutorial on Phylogenetics Human Rabbit Chicken
http://bioss.ac.uk/~dirk/talks/psnup_tutorial_phylogenetics.pdf

Phylogenetic Tree Computation Tutorial Overview
http://pga.lbl.gov/Workshop/April2002/lectures/Olken.pdf

MrBayes: A program for the Bayesian inference of phylogeny
http://golab.unl.edu/teaching/SBseminar/manual.pdf

Web sites providing software for the construction of phylogenetic trees

• BioEdit

• Coelocanth-Fish Out of Time

• Computational Biochemistry Research Group

• Digital Taxonomy

• Hennig 86

• Hyperclean from Bioinformatics Solutions, Inc.

• Memorial University of Newfoundland

• Mr. Bayes

• NONA

• Oxford University Evolutionary Biology Group

• Paleobiology Database

• PAUP

• Phylip Homepage

• Poy

• Sinauer Associates

• TNT-Tree Analysis Using New Technology

• Tree Base

• Treefinder

• Tree-Puzzle

• Tree View-Taxonomy and Systematics Group at Glasgow

• Washington University-List of Phylogeny Software