Multi-Modal Data Correspondence for the 4D Analysis of the Spine with Adolescent Idiopathic Scoliosis.

Adolescent idiopathic scoliosis is a three-dimensional spinal deformity that evolves during adolescence. Combined with static 3D X-ray acquisitions, novel approaches using motion capture allow for the analysis of the patient dynamics. However, as of today, they cannot provide an internal analysis of the spine in motion. In this study, we investigated the use of personalized kinematic avatars, created with observations of the outer (skin) and internal shape (3D spine) to infer the actual anatomic dynamics of the spine when driven by motion capture markers. Towards that end, we propose an approach to create a subject-specific digital twin from multi-modal data, namely, a surface scan of the back of the patient and a reconstruction of the 3D spine (EOS). We use radio-opaque markers to register the inner and outer observations. With respect to the previous work, our method does not rely on a precise palpation for the placement of the markers. We present the preliminary results on two cases, for which we acquired a second biplanar X-ray in a bending position. Our model can infer the spine motion from mocap markers with an accuracy below 1 cm on each anatomical axis and near 5 degrees in orientations.

Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation.

We present Seaview version 5, a multiplatform program to perform multiple alignment and phylogenetic tree building from molecular sequence data. Seaview provides network access to sequence databases, alignment with arbitrary algorithm, parsimony, distance and maximum likelihood tree building with PhyML, and display, printing, and copy-to-clipboard or to SVG files of rooted or unrooted, binary or multifurcating phylogenetic trees. While Seaview is primarily a program providing a graphical user interface to guide the user into performing desired analyses, Seaview possesses also a command-line mode adequate for user-provided scripts. Seaview version 5 introduces the ability to reconcile a gene tree with a reference species tree and use this reconciliation to root and rearrange the gene tree. Seaview is freely available at http://doua.prabi.fr/software/seaview .

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

MOTIVATION: Gene and species tree reconciliation methods are used to interpret gene trees, root them and correct uncertainties that are due to scarcity of signal in multiple sequence alignments. So far, reconciliation tools have not been integrated in standard phylogenetic software and they either lack performance on certain functions, or usability for biologists. RESULTS: We present Treerecs, a phylogenetic software based on duplication-loss reconciliation. Treerecs is simple to install and to use. It is fast and versatile, has a graphic output, and can be used along with methods for phylogenetic inference on multiple alignments like PLL and Seaview. AVAILABILITY AND IMPLEMENTATION: Treerecs is open-source. Its source code (C++, AGPLv3) and manuals are available from https://project.inria.fr/treerecs/.

RecPhyloXML: a format for reconciled gene trees.

Motivation: A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc.-along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Results: Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities. Availability and implementation: http://phylariane.univ-lyon1.fr/recphyloxml/.