[Protein families specific for plastoms in small taxonomy groups of algae and protozoa].

Protein clustering is useful for refinement of protein annotation as well as cluster finding by its phylogenetic profile. We performed clustering of plastid encoded proteins from Rhodophyta as well as other plastid containing species related to Rhodophyta branch on species tree. Data base for cluster finding by its phylogenetic profile is available on http://lab6.

[A fast algorithm to build a supertree with a set of gene trees].

Important desired properties of an algorithm to construct a supertree (species tree) by reconciling input trees are its low complexity and applicability to large biological data. In its common statement the problem is proved to be NP-hard, i.e.

[Attenuation regulation of amino acid and amino acyl-tRNA biosynthetic operons in bacteria: comparative genomics analysis].

We performed a large-scale search for attenuation regulation in bacteria based on two original computer programs modeling attenuation regulation and multiple alignment along a phylogenetic tree. The programs are available from http://lab6.iitp.

[Reconstructing genes evolution along a species tree].

A model and algorithm are proposed to infer evolution of a gene family, given the gene tree, with respect to species evolution, given the species tree. The model describes such evolution using the "nested tree" concept. Performance of the algorithm is verified on several orthologous protein groups.