Stable Flags and the Riemann-Hilbert Problem

We tackle the Riemann-Hilbert problem on the Riemann sphere as stalk-wise logarithmic modifications of the classical R\"ohrl-Deligne vector bundle. We show that the solutions of the Riemann-Hilbert problem are in bijection with some families of local filtrations which are stable under the prescribed monodromy maps. We introduce the notion of Birkhoff-Grothendieck trivialisation, and show that its computation corresponds to geodesic paths in some local affine Bruhat-Tits building. We use this to compute how the type of a bundle changes under stalk modifications, and give several corresponding algorithmic procedures.Comment: 39 page

Automatic detection of anchor points for multiple sequence alignment

<p>Abstract</p> <p>Background</p> <p>Determining beforehand specific positions to align (<it>anchor points</it>) has proved valuable for the accuracy of automated multiple sequence alignment (MSA) software. This feature can be used manually to include biological expertise, or automatically, usually by pairwise similarity searches. <it>Multiple </it>local similarities are be expected to be more adequate, as more biologically relevant. However, even good multiple local similarities can prove incompatible with the ordering of an alignment.</p> <p>Results</p> <p>We use a recently developed algorithm to detect multiple local similarities, which returns subsets of positions in the sequences sharing similar contexts of appearence. In this paper, we describe first how to get, with the help of this method, subsets of positions that could form partial columns in an alignment. We introduce next a graph-theoretic algorithm to detect (and remove) positions in the partial columns that are inconsistent with a multiple alignment. Partial columns can be used, for the time being, as guide only by a few MSA programs: ClustalW 2.0, DIALIGN 2 and T-Coffee. We perform tests on the effect of introducing these columns on the popular benchmark BAliBASE 3.</p> <p>Conclusions</p> <p>We show that the inclusion of our partial alignment columns, as anchor points, improve on the whole the accuracy of the aligner ClustalW on the benchmark BAliBASE 3.</p

MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences

International audienc

Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data

International audienceExplaining the evolution of animals requires ecological, developmental, paleontological, and phylogenetic considerations because organismal traits are affected by complex evolutionary processes. Modeling a plurality of processes, operating at distinct timescales on potentially interdependent traits, can benefit from approaches that are complementary treatments to phylogenetics. Here, we developed an inclusive network approach, implemented in the command line software ComponentGrapher, and analyzed trait co-occurrence of rhinocerotoid mammals. We identified stable, unstable, and pivotal traits, as well as traits contributing to complexes, that may follow to a common developmental regulation, that point to an early implementation of the postcranial Bauplan among rhinocerotoids. Strikingly, most identified traits are highly dissociable, used repeatedly in distinct combinations and in different taxa, which usually do not form clades. Therefore, the genes encoding these traits are likely recruited into novel gene regulation networks during the course of evolution. Our evo-systemic framework, generalizable to other evolved organizations, supports a pluralistic modeling of organismal evolution, including trees and networks