MGRA
Project lead: Pavel Avdeyev
MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes.
GitHub repository: https://github.com/ablab/mgra
Web-server: http://mgra.cblab.org
Genome Scaffolder
Project lead: Sergey Aganezov
GOS-ASM is a tool for multi-genome simultaneous co-scaffolding. Our framework aims at improving existing unfinished annotated assemblies by performing multi genome gene order analysis, with optional incorporation of phylogenetic relations between observed genomes and flanking repeats at the end of unfinished fragments.
Full project description: cblab.org/scaffolder
Dedicated software page: cblab.org/gos-asm
GitHub repository: github.com/aganezov/gos-asm
Issue tracker: youtrack.cblab.org/issues/GOSASM
Estimating of True Evolutionary Distance
Project lead: Nikita Alexeev
- N. Alexeev and M. A. Alekseyev. “Estimation of the True Evolutionary Distance under the Fragile Breakage Model”. BMC Genomics 18:Suppl 4 (2017), 356. doi:10.1186/s12864-017-3733-3 arXiv:1510.08002.
- N. Alexeev, R. Aidagulov, and M. A. Alekseyev. “A Computational Method for the Rate Estimation of Evolutionary Transpositions“. Lecture Notes in Computer Science 9043 (2015), pp. 471-480
Combinatorial Scoring of Phylogenetic Networks
Project lead: Nikita Alexeev
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for tree/network construction, it becomes important to measure how well constructed networks capture the given character relationship across the species.
In the current study, we propose a novel method for measuring the specificity of a given phylogenetic network in terms of the total number of distributions of character states at the leaves that the network may impose. While for binary phylogenetic trees, this number has an exact formula and depends only on the number of leaves and character states but not on the tree topology, the situation is much more complicated for non-binary trees or networks. Nevertheless, we develop an algorithm for combinatorial enumeration of such distributions, which is applicable for arbitrary trees and networks under some reasonable assumptions.
Sage Code: cactus_network
Publications:
- N. Alexeev and M. A. Alekseyev. “Combinatorial Scoring of Phylogenetic Networks”. Lecture Notes in Computer Science 9797 (2016), 560–572. doi:10.1007/978-3-319-42634-1_45 arXiv:1602.02841