This review revisits algorithms, tools, and workflows for sequence and phylogenetic analysis in the NGS-based omics era, with a focus on comparative performance and scenario-driven decision-making.
Taxonomic classification in metagenomics remains anchored in alignment-based methods and exact k-mer indexers, which provide calibrated, traceable species-level assignments at scale when reference coverage is comprehensive. This review synthesizes the progression of the field toward self-supervised, DNA-specific founda...
Andrey Felipe Schoier, Í. D. de Castro, M. Dorn· Computational biology and ch...· 0 citations
The next major release of RAxML-NG 2.0 introduces a plethora of new features: integrated model testing, multiple fast branch support metrics, automatic parallelization tuning, phylogenetic difficulty prediction, genotype evolution models, to name but the most important ones.
O. M. Kozlov, Anastasis Togkousidis, Christoph Stelz et al.· bioRxiv· 0 citations
This study conducted a comprehensive benchmark of the main bioinformatic tools and databases and demonstrated that even certain dominant genera remain difficult to detect, and that the quantification of all genera can be substantially over- or under-estimated, even when using optimal combinations of tools and reference...
Louis-Maël Guéguen, Alban Mathieu, Olivier Périn et al.· bioRxiv· 0 citations
MsaTM-DB is presented, a curated database comprising 965,545 loci from 420 eukaryotic phylogenomic studies, each annotated with 35 features spanning alignment properties, substitution parameters, and gene tree metrics that enable systematic investigation of heterogeneity in phylogenetic signals across diverse evolution...
Ancient and historical DNA has the potential to resolve many open questions in biology. While pipelines for processing ancient and historical DNA exist, none combine user-friendly, configurable processing with copy number variation tracking and targeted taxonomic profiling. Therefore, we developed pastForward, a fully...
Sarah Saadain, M. Kapun, R. Kofler· bioRxiv· 0 citations
Metagenomic analyses can be performed at multiple analytical levels, including read-based, assembly-based, and genome-resolved approaches, each capturing complementary biological information while introducing distinct analytical biases and trade-offs. However, existing workflows are commonly optimized for a single anal...
D. Corso, Edoardo Taccaliti, B. Barosa et al.· bioRxiv· 0 citations
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