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Databases

  • Bgee  •  Bgee is a database to compare expression patterns between animal species. Bgee addresses difficulties such as complex anatomies and diverse sources of data by the use of ontologies and the explicit representation of homology. Homology relationships are defined both between genes and between anatomical features. The main efforts are the annotation of anatomical and developmental terms and their homology relationships, and the annotation and statistical treatment of transcriptome data.  [less]
  • OMA  •  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. [less]
  • OrthoDB  •  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. [less]
  • ImmunoDB  •  A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families. [less]
  • miROrtho  •  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. [less]
  • PANDITplus  •  Along with sequence data for Pfam gene families and protein domains, PANDITplus provides access to data on protein interactions, functional and chemical pathway annotation, gene expression, and association with disease, and pre-computed estimates from evolutionary codon models. [less]
  • Selectome  •  Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment. [less]

Tools

  • OMA  •  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. [less]
  • ALF  •  ALF simulates a wide range of evolutionary forces that act on genomes, such as character substitutions, indels, gene duplication, gene loss, lateral gene transfer and genome rearrangement. [less]
  • AllAll  •  The AllAll server takes as input a set of protein sequences and returns various comparisons and visualizations- a distance-based phylogenetic tree, a split tree, some variation indices, some visualizations, the pairwise sequence distances and the most probable ancestral sequence. [less]
  • BayeScan  •  BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model. [less]
  • BIONJ  •  Neighbor Joining (NJ) algorithm improved for molecular sequences [less]
  • BLASTO  •  A modified BLAST, designed to query ortholog group data. It treats each ortholog group as a unit, and instead of providing a ranked list of individual sequence hits, it organizes and ranks the results by ortholog groups, which is often a much more desirable format for functional inference or evolutionary studies. [less]
  • Codon Suite  •  The CodonSuite server takes as input inframe coding DNA sequences and then performs various codon-based comparisons- codon-based alignments, a codon distance-based tree, SynPAM distance estimates and estimates of Nei and Gojoboris dN and dS.  [less]
  • CT-CBN  •  Continuous time conjunctive Bayesian networks (ct-cbn) are a family of graphical models describing the accumulation of mutations under order constraints. The software allows for the estimation of the network from cross-sectional data, such as mutation profiles of cancer or HIV patients.  [less]
  • DendroUPGMA  •  This tool creates a dendrogram from (a) a set of variables or (b) from a similarity matrix. The program calculates a similarity matrix (only for option a), transforms similarity coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm.  [less]
  • Evolutionary Trace Server (TraceSuite II)  •  This program maps evolutionary traces to structures [less]
  • fastsimcoal  •  fast sequential markov coalescent simulation of genomic data under complex evolutionary models [less]
  • Linear Classification  •  The Linear Classification server is a two-class classifier that finds the hyperplane that best splits a multi-dimensional space such that points of one class are on side of the plane and points of the other class are on the other. [less]
  • MLtree  •  MLtree is a software to compute maximum likelihood optimization of models of character evolution (either DNA or phenotypic ones) along the branches of a phylogenetic tree. It is assuming that the phylogenetic tree is known. [less]
  • MLTreeMap  •  MLTreeMap is a tool that employs full maximum likelihood to give insights into phylogenetic and functional properties of metagenomes and the underlying microbial communities. It does so by detecting and phylotyping a series of relevant marker genes on the submitted DNA fragments. Among these genes are protein coding phylogenetic markers, SSU rRNA genes and markers for important functional pathways. MLTreeMap is available as a web-server and as a stand-alone version. [less]
  • Newick Utilities  •  The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. [less]
  • PHYLIP  •  PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. [less]
  • Phylogenetic Tree  •  The Phylogenetic Tree server creates a distance or parsimony tree from a set of input sequences. It includes functionality for drawing the tree in several forms (radial, unrooted, rooted, phylogram or cladogram) with various other options.  [less]
  • Phylogeny.fr  •  Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. It runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. [less]
  • Phylogeny programs  •  Compilation of links to 390 phylogeny packages and about 50 free web servers, arranged by several criteria. [less]
  • RAxML  •  RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein's dnaml which is part of the PHYLIP package. [less]
  • SuperTree  •  SuperTree is a software to assemble phylogenetic trees into a more comprehensive one, called supertree, using specific algorithms [less]
  • The PhylOgenetic Web Repeater (POWER)  •  The PhylOgenetic Web Repeater (POWER) allows users performing phylogenetic analysis with molecular data by most programs of PHYLIP package repeatedly. POWER provide two pipelines to process the analysis. One of them includes multiple sequence alignment (MSA) at the begining of the pipeline whereas the other begin phylogenetic analysis with aligned sequence. [less]
  • TreeGen  •  The TreeGen server takes as input a user-generated distance matrix and creates from it a distance-based phylogenetic tree. [less]
  • Vertex Cover  •  The VertexCover server takes as input a graph defined by two sets- a set of vertices and a set of edges. It returns the smallest set of vertices, S, such that each edge is incident to one vertex in S. [less]