Databases

• Bgee • gene expression patterns comparison • [more]
  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]

• ImmunoDB • insect immune-related genes and gene families • [more]
  ImmunoDB  •  A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families. [less]
• miROrtho • catalogue of animal microRNA genes • [more]
  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]
• OMA • orthology inference among complete genomes. • [more]
  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 • Hierarchical catalog of eukaryotic orthologs • [more]
  OrthoDB  •  OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus 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. [less]
• PANDITplus • protein families and domains resources • [more]
  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 • positive selection • [more]
  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

• ALF • simulation of genome evolution • [more]
  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 • protein sequences comparisons • [more]
  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 • identify natural selection • [more]
  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]
• Codon Suite • codon-based sequence analysis • [more]
  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 • estimate conjunctive Bayesian networks • [more]
  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]
• fastsimcoal • coalescent simulation of genomic data • [more]
  fastsimcoal  •  fast sequential markov coalescent simulation of genomic data under complex evolutionary models [less]
• Linear Classification • simple linear classification • [more]
  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 • maximum likelihood optimization • [more]
  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 • phylogenetics and functionalities of metagenomes • [more]
  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 • high-throughput phylogenetic tree processing • [more]
  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]
• OMA • orthology inference among complete genomes. • [more]
  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]
• Phylogenetic Tree • phylogenetic tree construction and printing • [more]
  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]
• RAxML • ML inference of large phylogenetic trees • [more]
  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 • assemble phylogenetic trees • [more]
  SuperTree  •  SuperTree is a software to assemble phylogenetic trees into a more comprehensive one, called supertree, using specific algorithms [less]
• TreeGen • phylogenetic tree from distance matrix • [more]
  TreeGen  •  The TreeGen server takes as input a user-generated distance matrix and creates from it a distance-based phylogenetic tree. [less]
• Vertex Cover • resolves a vertex cover problem • [more]
  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]