Databases and Tools
These are some resources that we have developed within our group. Most of them originate from our own needs in our daily research. If possible, we implement our own solutions in a form that can be used by all the community. We are open for ideas for improving or extending these tools.
Click on the icon below to go to the resource's website.
PhylomeDB is a public database for complete collections of gene phylogenies (phylomes).
It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions based on the analysis of the phylogenetic trees.
trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment
It also includes readAl, a format converter between most alignment formats
ETE (Environment for Tree Exploration) is a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. Besides a broad set of tree handling options, ETE’s current version provides specific methods to analyze phylogenetic and clustering trees. It also supports large tree data structures, node annotation, independent editing and analysis of tree partitions, and the association of trees with external data such as multiple sequence alignments or numerical matrices.
|Deathbase is a database of proteins involved in cell death. It compiles relevant data on the function, structure and evolution of proteins involved in apoptosis and other forms of cell death in several organisms. Information contained in this database is subjected to manual curation. You can contribute to maintain the DeathBase by editing the wikipage for any protein.|
|MetaPhOrs is a public repository of phylogeny-based orthology and paralogy predictions that were computed using resources available in seven popular homology prediction services (PhylomeDB, EnsemblCompara, EggNOG, OrthoMCL, COG, Fungal Orthogroups, and TreeFam). Currently above 306 millions of unique homologous protein pairs are deposited in MetaPhOrs database. These predictions were retrieved from 705 123 phylogenetic trees for 829 genomes. For each prediction, MetaPhOrs provides a Consistency Score and Evidence Level describing its goodness, together with number of trees and links to their source databases.|
|TreeKO is a python package used to compare phylogenetic trees|
Please, if you use our software and databases, do not forget to refer to them in your publications.
DeathBase: a database on structure, evolution and function of proteins involved in apoptosis and other forms of cell death.. Cell Death Differ.. 17:735–736.. 2010.
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.. Bioinformatics. 25:1972–1973.. 2009.