How to build phylogenetic species trees with OMA [version 2; peer review: 2 approved with reservations]

Knowledge of species phylogeny is critical to many fields of biology. In an era of genome data availability, the most common way to make a phylogenetic species tree is by using multiple protein-coding genes, conserved in multiple species. This methodology is composed of several steps: orthology inference, multiple sequence alignment and inference of the phylogeny with dedicated tools. This can be a difficult task, and orthology inference, in particular, is usually computationally intensive and error prone if done ad hoc. This tutorial provides protocols to make use of OMA Orthologous Groups, a set of genes all orthologous to each other, to infer a phylogenetic species tree. It is designed to be user-friendly and computationally inexpensive, by providing two options: (1) Using only precomputed groups with species available on the OMA Browser, or (2) Computing orthologs using OMA Standalone for additional species, with the option of using precomputed orthology relations for those present in OMA. A protocol for downstream analyses is provided as well, including creating a supermatrix, tree inference, and visualization. All protocols use publicly available software, and we provide scripts and code snippets to facilitate data handling. The protocols are accompanied with practical examples

Clinical bioinformatics for microbial genomics and metagenomics:an ESCMID Postgraduate Technical Workshop

The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) workshop on genomics and metagenomics was held in Lausanne from 9th to 12th September 2019. As many as 68 participants from 20 countries from all 5 continents participated to this postgraduate technical workshop. During 4 days, the participants shared their time between conferences on various topics related to the implementation of genomics and metagenomics in a clinical diagnostic laboratory. These included talks from the clinics and talks from bioinformatic experts. A significant time was also dedicated to practicals covering various aspects of the data analysis of NGS sequences (quality check, annotation of virulence and antibiotic resistance genes, taxonomic assignment of amplicons, strain typing, …). This ESCMID meeting co-organized by A Lebrand and G Greub, with the help of the European Study Group for Genomics ad Molecular Diagnostics (ESGMD) provided a unique opportunity to exchange knowledge and ideas on the most recent bioinformatic approaches, as well as how to report such NGS results in diagnostic laboratories. This meeting report summarizes the key messages of this meeting

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new features in the OMA web browser. Notable improvements include: (i) a scalable, interactive viewer for hierarchical orthologous groups; (ii) protein domain annotations and domain-based links between orthologous groups; (iii) functionality to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate incorporation of OMA analyses in computational pipelines and integration with other bioinformatic resources. OMA can be freely accessed at https://omabrowser.org

Data and Scripts: Antibacterial inhibitors targeting the lipoprotein transport pathway

The data presented here are the sequences used to construct the phylogenetic tree in Figure 3. Collected sequences are presented in fasta format (fa ending). Alignement is in fasta (aln ending). Phylogenetic trees are as nwk strings with bootstrap (contree ending). Moreover, data filtering script is present as jupyter notebook. Metadata is present as csv file and other log files are available to highlight the iqtree tree inference.</p

Bifurcation search via feedback loop breaking in biochemical signaling pathways with time delay

We develop a method to locate bifurcations in time delay systems with a potentially high-dimensional parameter space. It is based on the feedback loop breaking approach that we developed and applied earlier for bifurcation search in ordinary differential equations. The method is particularly suited for the analysis of biological networks, for example to determine which parameters are relevant for complex dynamical behavior in such networks. To illustrate the benefits that this approach yields for biological network analysis, we apply it to study the effect of parameter variations on oscillations in a model of the MAP kinase cascade with a time delay. © 2011 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society.status: publishe

Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree

Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly and annotation quality, especially for large datasets. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes and bypasses traditional steps in phylogeny inference, such as genome assembly, annotation and all-versus-all sequence comparisons, while retaining accuracy. In a benchmark encompassing a broad variety of datasets, Read2Tree is 10-100 times faster than assembly-based approaches and in most cases more accurate-the exception being when sequencing coverage is high and reference species very distant. Here, to illustrate the broad applicability of the tool, we reconstruct a yeast tree of life of 435 species spanning 590 million years of evolution. We also apply Read2Tree to >10,000 Coronaviridae samples, accurately classifying highly diverse animal samples and near-identical severe acute respiratory syndrome coronavirus 2 sequences on a single tree. The speed, accuracy and versatility of Read2Tree enable comparative genomics at scale.ISSN:1546-1696ISSN:1087-015

Additional file 2: of Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution

Supplementary Tables S1 to S7. (DOCX 24 kb

Additional file 3: of Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution

All vs all search for 901 skeletogenic genes. This file includes the detailed results of Fig. 2 and Additional file 1: Figure S5 to show in detail which genes are parts of the different overlaps between the four species. (XLSX 197 kb