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Results for « phylogeny »

RDP / Ribosomal Database Project
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Provides aligned and annotated ribosomal RNA (rRNA) gene sequence data, along with tools to allow researchers to analyse their own rRNA gene sequences. RDP offers tools for browsing and searching the data collections, for taxonomic classification and nearest neighbour search, for primer-probe testing and for tree building. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics.
PHYLIP / the PHYLogeny Inference Package
A free package of programs for inferring phylogenies. It can infer phylogenies by parsimony, compatibility, distance matrix methods, and likelihood. It also computes consensus trees, compute distances between trees, draw trees, resample data sets by bootstrapping or jackknifing, edit trees, and compute distance matrices. PHYLIP handles data that are nucleotide sequences, protein sequences, gene frequencies, restriction sites, restriction fragments, distances, discrete characters, and continuous characters.
CSI Phylogeny / Call SNPs & Infer Phylogeny
Identifies variations in whole genome sequencing (WGS) reads and conducts phylogenetic analysis of isolates. CSI Phylogeny is a webserver which calls and filters the single nucleotide polymorphisms (SNPs), does site validation and infers a phylogeny based on the concatenated alignment of the SNPs. The method was evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent) and overcomes the systematic biases caused by the sequencers.
REALPHY / Reference sequence Alignment-based Phylogeny builder
Aligns raw short-sequence reads to one or more reference sequences. REALPHY can successfully avoid biases from mapping to a single reference by implementing a procedure for merging alignments obtained by mapping to multiple reference genomes into a single nonredundant alignment. It was designed to reconstruct phylogenies for microbial genomes, that is, bacterial genomes and single cell eukaryotes such as fungi, but it can in principle be equally applied to data from higher eukaryotic organisms.
MARATHON / copy nuMber vARiAtion and Tumor pHylOgeNy
Enables copy number profiling and downstream analyses in disease genetic studies. MARATHON is a pipeline that gathers statistical software: CODEX and CODEX2 perform read depth normalization for total copy number profiling, iCNV receives read depth normalized by CODEX/CODEX2, FALCON and FALCON-X perform allele-specific copy number (ASCN) analysis and Canopy receives input from FALCON/FALCON-X to perform tumor phylogeny reconstruction. The pipeline adapts to different study designs and research goals.
SPRUCE / Somatic Phylogeny Reconstruction Using Combinatorial Enumeration
Infers a multi-state perfect phylogeny describing the evolutionary history of the somatic mutations (Single-Nucleotide Variations (SNV)s and Copy-Number Aberrations (CNAs)) of a tumor given multi-sample bulk sequencing data. SPRUCE addresses complexities in simultaneous analysis of SNVs and CNAs. Importantly, this tool relies on the infinite alleles, or no-homoplasy, assumption. Finally, SPRUCE gives additional insights into intra-tumor heterogeneity.
RADIS / analysis of RAD-seq data for InterSpecific phylogeny
Automates and standardizes the analyses of RAD-seq data for phylogenetic inference. Users of RADIS can let their raw Illumina data be processed up to phylogenetic tree inference, or stop (and restart) the process at some point. Different values for key parameters can be explored in a single analysis (e.g. loci building, sample/loci selection), making possible a thorough exploration of data. RADIS relies on Stacks for demultiplexing of data, removing PCR duplicates and building individual and catalog loci. Scripts have been specifically written for trimming of reads and loci/sample selection. Finally, RAxML is used for phylogenetic inferences, though other software may be utilised.
MrBayes
Estimates the posterior distribution of model parameters. MrBayes is a program that performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo (MCMC). It can infer ancestral states while accommodating uncertainty about the phylogenetic tree and model parameters. It also implements several methods for relaxing the assumption of equal rates across sites, including gamma-distributed rate variation. It can be used to test various topological hypotheses or substitution models against each other.
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Results for « phylogeny »

Cichlid phylogeny search tool
Contains data of the evolutionary relationship of each cichlid protein to its nearest human and zebrafish protein. Cichlid phylogeny search tool can help cichlid researchers to predict biological and protein function for a given cichlid gene, understanding the evolutionary history of a given cichlid gene, identifying recently duplicated cichlid genes, or performing genome-wide analysis in cichlids that relies on using databases generated from other species.
SRPDB / Signal Recognition Particle Database
Provides aligned, annotated and phylogenetically ordered sequences of the Signal recognition particle (SRP) components. SRPDB is a database that provides alphabetically and phylogenetically ordered lists of SRP RNA and SRP protein sequences. This online resource is also organized for additional proteins that play a role in SRP-mediated protein transport or are related to SRP components. The SRPDB lists 115 sequences from all phylogenetic groups.
OrthoMCL-DB
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Contains ortholog groups for most completely sequenced and annotated eukaryotes for a number of completely sequenced and annotated prokaryotes. OrthoMCL-DB provides a wealth of functionality, including domain architecture for each group, phyletic patterns for each group and advanced querying, including phylogenetic pattern searches. The database gives also access to OrthoMCL, which groups proteins into “ortholog groups” (i.e. set of proteins across one or more species that represent putative orthologs and in-paralogs).
CGD / Candida Genome Database
Provides gene, protein and sequence information for multiple Candida species. CGD contains web-based tools for accessing, analyzing and exploring these data, to facilitate and accelerate research into Candida pathogenesis and biology. Locus pages comprise a summary view along with several additional tabs that display more detailed information, including phenotype details, Gene Ontology term curation, protein product details for coding genes, notes on changes to the sequence or structure of the gene, a comprehensive reference list and the Homology Information tab, a place where phylogeny- and similarity-related data may be examined and evaluated.
GWIPS-viz / Genome Wide Information on Protein Synthesis visualized
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Provides access to the genomic alignments of public ribo-seq reads in conjunction with mRNA-seq reads along with relevant annotation tracks. GWIPS-viz is a specialized ribo-seq browser allowing researchers to support ribo-seq evidence for alternative proteoforms inferred from phylogenetic analysis or detect with proteomics or other experimental techniques. It can be used as a support tool for predictions based on other approaches and for generating hypotheses that can be tested using methods other than ribo-seq.
TCDB / The Transporter Classification Database
A freely accessible reference database for transport protein research, which provides structural, functional, mechanistic, evolutionary and disease/medical information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB). It consists of more than 10 000 non-redundant transport systems with more than 11 000 reference citations, classified into over 1000 transporter families. Transporters in TCDB can be single or multi-component systems, categorized in a functional/phylogenetic hierarchical system of classes, subclasses, families, subfamilies and transport systems. TCDB also includes updated software designed to analyze the distinctive features of transport proteins, extending its usefulness.
TimeTree
Offers a public knowledge-base for information on the tree-of-life and its evolutionary timescale. TimeTree is a web-based resource for researchers and educators from all fields of science to assist in the discovery of patterns and the formulation of hypotheses, or simply to learn about the timetree of life. The home page describes the database and presents a choice of two user-query forms: finding the divergence of two taxa, and finding all time estimates from a particular author. The current version contains timetrees reported from molecular clock analyses in 910 published studies and 17 341 species that span the diversity of life. TimeTree interprets complex and hierarchical data from these studies for each user query, which can be launched using an iPhone application, in addition to the website.
HmtDB / Human Mitochondrial Database
Supports population genetics and mitochondrial disease studies. HmtDB hosts human mitochondrial genome sequences annotated with population and variability data, the latter being estimated through the application of the SiteVar/MitVarProt programs, based on site-specific nucleotide and aminoacid variability calculations. The annotations are manually curated thus adding value to the quality of the information provided to the end-user. Classifier tools implemented in HmtDB allow the prediction of the haplogroup for any human mitochondrial genome currently stored in HmtDB or externally submitted de novo by an end-user. Haplogroup definition is based on the Phylotree system. End-users accessing HmtDB are hence allowed to: (i) browse the database through a multi-criterion query system; (ii) analyse their own human mitochondrial sequences via the classify tool or by downloading the mt-classifier tool; (iii) download multi-alignments with reference genomes as well as variability data.
GreenPhylDB
Provides a database for comparative genomic analysis full genomes. GreenPhylDB is a web accessible, user-friendly comparative platform for plant genomes studies including family classification, phylogenomic analysis information and cross-reference links. It comes with a set of dedicated tools, InterPro, KEGG, TAIR or sequences ID as queries. It also integrates a dedicated phylogenomics tool, GreenPhyl Ortholog Search Tool (GOST), to search orthologs using protein sequences from other plant species.
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Results for « phylogeny »

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