¶ Phylogeny
¶ Phylogeny Related Resources
proGenomes Consistently annotated bacterial and archaeal genomes- ToLWeb Tree of Life Web Project is a collection of information about biodiversity
¶ Phylogeny Tools
- BCdatabaser Pipeline to create reference databases for arbitrary markers and taxonomic groups from NCBI data
- GraPhlAn Tool that produces high-quality, compact visualizations of microbial genomes
- Graph Splitting Phylogenetic analysis method, which can effectively resolve early evolution of protein families
- IQ-TREE Efficient software for phylogenomic inference
- LeBIBI-QBPP Quick Bioinformatic Phylogeny of Prokaryotes web-server
- MEGASoftware Software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees
- NGPhylogeny Reconstructing and analysing phylogenetic relationships
- Phylemon Web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
- Simple Phylogeny Provides access to phylogenetic tree generation methods from the ClustalW2
- TREND Resource that can calculate gene neighborhoods
¶ Phylogenetic Distribution Tools
- AnnoTree Visualization of genome annotations across large phylogenetic trees
- JGI-IMG/Microbes Community resource for analysis and annotation of genome
- JGI-IMG/Virus Community resource for analysis and annotation of genome
- KEGG Ortholog Cluster Database of ortholog clusters (OCs) based on the whole genome comparison
- MBGD Workbench system for comparative analysis of completely sequenced microbial genomes
- OrthoDB OrthoDB presents a catalog of orthologous protein-coding genes
- OrthoInspector Inference of orthologous relationships between protein coding-genes
- Phylogenes Pre-computed phylogenetic trees of gene families alongside experimental gene function data
¶ Visualizing Tree
- ETE-Toolkit A Python framework for the analysis and visualization of trees
- EvolView Easy-to-use online tool for displaying, managing and customizing phylogenetic trees
- iTOL Online tool for the display, annotation and management of phylogenetic trees
- Lifemap Tool allowing the exploration of a complete representation of the Tree of Life
- Phandango Interactive viewer for bacterial population genomics
- Phylodendron Tool for printing phylogenetic trees