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Showing 9 records out of 9 total

Categories: genomics, evolutionary biology - Software type(s): website - database/tool
CEGA (Conserved Elements from Genomic Alignments) provides access to precomputed sets of conserved sequences from different species and at different levels of the vertebrate phylogeny.
Categories: evolutionary biology - Software type(s): website - tool
The Coev-Web platform is a user-friendly interface of the command-line program Coev. The platform allows the evaluation of coevolving positions and their evolutionary profile based on the aligned sequences and a phylogenetic tree. It can also simulate coevolving pairs of positions along a given phylogenetic tree.
Categories: genomics, (characterisation/annotation), evolutionary biology - Software type(s): website - database
A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.
Categories: genomics, (characterisation/annotation), evolutionary biology - Software type(s): website - database
miROrtho contains predictions of precursor miRNA genes covering many animal genomes combining evidence from sequence homology and Support Vector Machine classifiers. We provide both consistent extrapolation of already known miRBase families and novel miRNA predictions by our SVM and orthology pipeline.
Categories: genomics, (characterisation/annotation), evolutionary biology - Software type(s): website, CLI, API - database/tool
OMA is a project that aims to identify orthologs among publicly available, complete genomes. With many hundreds of genomes analyzed to date, OMA is one of the largest projects of its kind.
Categories: genomics, (characterisation/annotation), evolutionary biology - Software type(s): website - database
Catalog of eukaryotic orthologous protein-coding genes. OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. Available protein descriptors, together with Gene Ontology and InterPro attributes, serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive database querying. Data sources include proteomes from arthropods, fungi, vertebrates and basal metazoans.
Categories: evolutionary biology - Software type(s): website, library - tool
Phylo.io is a state of the art tool for visualising and comparing phylogenetic trees on the web. It can be used to view a single tree, or compare the internal structure of two differently inferred trees for the same group of taxons. Phylo.io includes a number of useful features to make the viewing and comparing of even very large trees extremely easy.
Categories: evolutionary biology - Software type(s): website, CLI - tool
REALPHY - The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data. The user only has to provide genome sequences in FASTA, GenBank or FASTQ formats. From these sequences phylogenetic trees are inferred via PhyML. The alignments, tree files and information on SNPs and deleted sites will be available for download after the analysis is finished.
Categories: proteomics, genomics, (sequence alignment), evolutionary biology - Software type(s): website - database/tool
The SwissTree project aims to provide a collection of 100 Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure. SwissTree is used for benchmarking at the Orthology Benchmarking web service.