SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
...cified in META files (see Manual) or specific variant information as specified in VAR files (see Manual) and NEWICK files for specifying clonal phylogenetic trees in cancer. SVEngine ou...1399 days ago
IRscope: an online program to visualize the junction sites of chloroplast genomes
eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences.1254 days ago
PaReBrick: PArallel REarrangements and BReaks identification toolkit
PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for...937 days ago
844 days ago
Genomicus: genome browser that enables users to navigate in genomes in several dimensions
...nced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest. All the d...794 days ago
homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
...omologizer, please cite the paper in which we first describe the method: Freyman, W.A., Johnson, M.G., and C.J. Rothfels. 2022. Homologizer: phylogenetic phasing of gene copies into p...334 days ago
Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes
Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of prote...enerated from multi-copy gene families. For phylogenetic inference, users can choose a...tings to retain high-quality alignments for phylogenetic inference. The workflow produ...72 days ago
MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction
...ncing reads and enables the construction of phylogenetic trees based on the resultant...-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast...vels, proving itself as a powerful tool for phylogenetic tree construction.25 days ago