NGSEP 4: Efficient and accurate identification of orthogroups and whole-genome alignment.

Whole-genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment. Our results showed that the NGSEP algorithm for orthogroups identification has competitive accuracy and efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. NGSEP 4 also includes a new graphical user interface based on the JavaFX technology. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics.

Urban Transformations and Health: Methods for TrUST-a Natural Experiment Evaluating the Impacts of a Mass Transit Cable Car in Bogotá, Colombia.

Background: Cable cars provide urban mobility benefits for vulnerable populations. However, no evaluation has assessed cable cars' impact from a health perspective. TransMiCable in Bogotá, Colombia, provides a unique opportunity to (1) assess the effects of its implementation on the environmental and social determinants of health (microenvironment pollution, transport accessibility, physical environment, employment, social capital, and leisure time), physical activity, and health outcomes (health-related quality of life, respiratory diseases, and homicides); and (2) use citizen science methods to identify, prioritize, and communicate the most salient negative and positive features impacting health and quality of life in TransMiCable's area, as well as facilitate a consensus and advocacy-building change process among community members, policymakers, and academic researchers. Methods: TrUST (In Spanish: Transformaciones Urbanas y Salud: el caso de TransMiCable en Bogotá) is a quasi-experimental study using a mixed-methods approach. The intervention group includes adults from Ciudad Bolívar, the area of influence of TransMiCable. The control group includes adults from San Cristóbal, an area of future expansion for TransMiCable. A conceptual framework was developed through group-model building. Outcomes related to environmental and social determinants of health as well as health outcomes are assessed using questionnaires (health outcomes, physical activity, and perceptions), secondary data (crime and respiratory outcomes) use of portable devices (air pollution exposure and accelerometry), mobility tracking apps (for transport trajectories), and direct observation (parks). The Stanford Healthy Neighborhood Discovery Tool is being used to capture residents' perceptions of their physical and social environments as part of the citizen science component of the investigation. Discussion: TrUST is innovative in its use of a mixed-methods, and interdisciplinary research approach, and in its systematic engagement of citizens and policymakers throughout the design and evaluation process. This study will help to understand better how to maximize health benefits and minimize unintended negative consequences of TransMiCable.