Skip to main page content
U.S. flag

An official website of the United States government

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Feb 15;36(4):1286-1288.
doi: 10.1093/bioinformatics/btz710.

Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages

Adrián A Davín  1   2 , Théo Tricou  3 , Eric Tannier  3   4 , Damien M de Vienne  3 , Gergely J Szöllősi  1   2   5
Affiliations

Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages

Adrián A Davín et al. Bioinformatics. .

Abstract

Summary: Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have not to date been combined in a single simulator, such as the possibility of generating species trees with a pre-defined variation of speciation and extinction rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree-species tree reconciliations.

Availability and implementation: Source code and manual are freely available in https://github.com/AADavin/ZOMBI/.

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Overview of the three steps of the Zombi simulator. (A) In T mode, Zombi simulates a species tree using a birth-death process and outputs the pruned version of it by removing extinct lineages. In this example, lineages n3 and n8 go extinct before the simulation ends. (B) in G mode, a circular genome evolves within the branches of the complete species tree obtained with the T mode by Duplications (D), Originations (O), Inversions (I), Transpositions (P), Losses (L) and Transfers (T) of genes. The simulation starts with the initial genome (IG) containing a number of genes determined by the user (5 in this example, represented by the coloured circles). Each gene has an orientation (+ or -) that is determined randomly and represents the direction of the gene in the coding strand. Several events affecting different genes and their impact on the genome structure are indicated next to the branches where they occur. The inversion events not only modify the positions of the genes but also change their orientation. (C) In S mode, Zombi can be used to simulate codon, nucleotides and amino acids along the branches of the gene family trees. Here, the gene tree of the grey coloured gene family from B has been depicted
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Abby S.S. et al. (2012) Lateral gene transfer as a support for the tree of life. Proc. Natl. Acad. Sci. USA, 109, 4962. - PMC - PubMed
    1. Beiko R.G., Charlebois R.L. (2007) A simulation test bed for hypotheses of genome evolution. Bioinformatics, 23, 825–831. - PubMed
    1. Biller P. et al. (2016) Breaking good: accounting for fragility of genomic regions in rearrangement distance estimation. Genome Biol. Evol., 8, 1427–1439. - PMC - PubMed
    1. Boussau B. et al. (2008) Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of bacteria. BMC Evol. Biol., 8, 272.. - PMC - PubMed
    1. Carvajal-Rodríguez A. (2008) Simulation of genomes: a review. Curr. Genomics, 9, 155–159. - PMC - PubMed

Publication types

Substances