Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites
J Integr Bioinform. 2024 Mar 27. doi: 10.1515/jib-2023-0046. Online ahead of print.ABSTRACTThe vast amount of genome sequence data that is available, and that is predicted to drastically increase in the near future, can only be efficiently dealt with by building automated pipelines. Indeed, the Earth Biogenome Project will produce high-quality reference genome sequences for all 1.8 million named living eukaryote species, providing unprecedented insight into the evolution of genes and gene families, and thus on biological issues. Here, new modules for gene annotation, further BLAST search algorithms, further multiple sequen...
Source: Journal of integrative bioinformatics - March 26, 2024 Category: Bioinformatics Authors: Hugo L ópez-Fernández Miguel Pinto Cristina P Vieira Pedro Duque Miguel Reboiro-Jato Jorge Vieira Source Type: research

MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps
We present MetaLo, an open-source Python package that enables the coupling of Boolean models inferred from process description MIMs with generic core metabolic networks. MetaLo provides a framework to study the impact of signaling cascades, gene regulation processes, and metabolic flux distribution of central energy production pathways. MetaLo computes the Boolean model's asynchronous asymptotic behavior, through the identification of trap-spaces, and extracts metabolic constraints to contextualize the generic metabolic network. MetaLo is able to handle large-scale Boolean models and genome-scale metabolic models without r...
Source: Journal of integrative bioinformatics - February 5, 2024 Category: Bioinformatics Authors: Sahar Aghakhani Anna Niarakis Sylvain Soliman Source Type: research