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Aevol-9: A simulation platform to decipher the evolution of genome architecture

Luiselli, J.; Parsons, D.; Galle, R.; Banse, P.; Rouzaud-Cornabas, J.; Beslon, G.

2025-04-10 evolutionary biology
10.1101/2025.04.10.648095 bioRxiv
Show abstract

Aevol is a forward-in-time simulator of genome architecture. It simulates a population of individuals, each with an explicit genome whose sequence and architecture can be modified by various mutational operators, including substitutions, indels, and large-scale chromosomal rearrangements. This enables performing in silico experiments to decipher the effects of evolutionary conditions (e.g. population size, selection strength, mutation rates, and biases) on genome organization.

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 0.8%
25.8%
Similar papers in this journal
2
Molecular Biology and Evolution
◐ 542 papers in training set
Top 0.7%
10.3%
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3
PLOS Computational Biology
● 1863 papers in training set
Top 6%
6.1%
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4
Methods in Ecology and Evolution
○ 176 papers in training set
Top 0.5%
5.0%
Similar papers in this journal
5
Peer Community Journal
● 281 papers in training set
Top 0.9%
5.0%
Similar papers in this journal
50% of probability mass above
6
eLife
● 5828 papers in training set
Top 31%
3.9%
7
iScience
○ 1154 papers in training set
Top 8%
3.1%
8
Virus Evolution
◐ 155 papers in training set
Top 0.6%
2.7%
9
G3 Genes|Genomes|Genetics
◐ 351 papers in training set
Top 2%
2.4%
10
GENETICS
◐ 483 papers in training set
Top 2%
2.1%
11
G3: Genes, Genomes, Genetics
◐ 252 papers in training set
Top 2%
2.1%
12
Journal of Open Source Software
● 25 papers in training set
Top 0.2%
1.9%
13
Genome Biology and Evolution
◐ 338 papers in training set
Top 2%
1.9%
14
Nature Communications
○ 5641 papers in training set
Top 47%
1.5%
15
Genome Biology
○ 637 papers in training set
Top 7%
1.3%
16
PeerJ
◐ 308 papers in training set
Top 7%
1.3%
17
Molecular Ecology Resources
○ 171 papers in training set
Top 2%
1.1%
18
GigaScience
◐ 212 papers in training set
Top 3%
1.1%
19
Bioinformatics Advances
◐ 203 papers in training set
Top 4%
1.1%
20
Genome Research
● 468 papers in training set
Top 6%
0.9%
21
Scientific Reports
○ 3612 papers in training set
Top 74%
0.8%
22
BMC Genomics
○ 406 papers in training set
Top 8%
0.8%
23
Ecology and Evolution
○ 267 papers in training set
Top 5%
0.8%
24
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 4%
0.8%
25
PLOS ONE
● 5266 papers in training set
Top 60%
0.8%
26
Life Science Alliance
● 285 papers in training set
Top 10%
0.6%
27
Systematic Biology
◐ 144 papers in training set
Top 0.8%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.