## 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.com/aganezov/gos-asm**

GitHub repository:

GitHub repository:

**Issue tracker:**youtrack.cblab.org/issues/GOSASM

## Estimating of True Evolutionary Distance

Project lead: Nikita Alexeev

**Publications:**

- N. Alexeev and M. A. Alekseyev. “Estimation of the True Evolutionary Distance under the Fragile Breakage Model”.
*BMC Genomics*18:Suppl 4 (2017), 356. - 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