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Unclassified software tools | Genome annotation

PAIDB
Dataset

PAIDB PAthogenicity Island DataBase

A comprehensive relational database of all the reported pathogenicity islands…

A comprehensive relational database of all the reported pathogenicity islands (PAIs) and potential PAI regions which were predicted by a method that combines feature-based analysis and…

DoriC
Dataset

DoriC Database of oriC regions in Bacterial and Archaeal genomes

Stores origins of replication (oriC) regions in bacterial genomes. DoriC is an…

Stores origins of replication (oriC) regions in bacterial genomes. DoriC is an online database that contains oriCs in more than 1520 bacterial and in more than 80 archaeal genomes. It also includes…

ACE
Desktop

ACE Assessing Changes to Exons

Identifies possible functional changes in gene structure that may result from…

Identifies possible functional changes in gene structure that may result from sequence variants. ACE converts phased genotype calls to a collection of explicit haplotype sequences, maps transcript…

Isochore
Web
Desktop

Isochore

Plots isochores in DNA sequences. Isochore is an EMBOSS web app that needs a…

Plots isochores in DNA sequences. Isochore is an EMBOSS web app that needs a nucleic acid sequence in FASTA, UniProtKB or Swiss-Prot. It plots GC content in windows over a DNA sequence. The data may…

Vizardous
Desktop

Vizardous

Allows exploration, analysis and interpretation of single-cell data.…

Allows exploration, analysis and interpretation of single-cell data. Vizardous’ core functionality is to visualize time-resolved, single-cell and population data. It can be used for the automated…

DASACT
Desktop

DASACT Decision Aiding Software for Axiomatic Consensus Theory

Assists practitioners on choosing the most appropriate consensus function for…

Assists practitioners on choosing the most appropriate consensus function for generating consensus trees. The decision aiding is made on the user’s preference on the nine axiomatic properties, any…

GeneBase
Dataset

GeneBase

Generates a fully structured local database with an intuitive user-friendly…

Generates a fully structured local database with an intuitive user-friendly graphic interface for personal computers. GeneBase is a full parser of the National Center for Biotechnology Information…

5'SAGE
Dataset

5'SAGE

Provides transcription start sites and frequencies of individual genes.…

Provides transcription start sites and frequencies of individual genes. 5’SAGE can be queried on the accession numbers of sequences in RefSeq, cluster identifiers in UniGene or symbol names, such…

MitoPhAST
Desktop

MitoPhAST Mitogenome Phylogenetic Analysis of Sequences Tool

Identifies annotated protein-coding gene features, generates a maximum…

Identifies annotated protein-coding gene features, generates a maximum likelihood phylogenetic tree and reports various mitochondrial genes and sequence information in a table format. The recovered…

Clockstar
Desktop

Clockstar

An R package for phylogenetic molecular clock analyses of multi-gene data sets.…

An R package for phylogenetic molecular clock analyses of multi-gene data sets. ClockstaR uses the patterns of among lineage rate variation for the different genes to select the clock-partitioning…

TreeFix
Desktop

TreeFix

Combines sequence data and species tree information and improve gene tree…

Combines sequence data and species tree information and improve gene tree reconstructions. TreeFix consists of three basic components: (i) a test of statistical equivalence to filter out gene tree…

ytool
Desktop

ytool

A standalone pipeline for retrieving human Y chromosomal single nucleotide…

A standalone pipeline for retrieving human Y chromosomal single nucleotide polymorphisms (SNPs) information in DNA chip in order to perform phylogenetic analyses. It consists of two modules: PLINK…

DNAtraffic
Dataset

DNAtraffic

Provides information about genome dynamics during the cell life. DNAtraffic is…

Provides information about genome dynamics during the cell life. DNAtraffic is an annotated resource that contains data about: (i) DNA metabolism; (ii) proteins enrolled in widely understanding the…

RefineTree
Web

RefineTree

Implements a gene tree generation method called ProfileNJ. RefineTree takes a…

Implements a gene tree generation method called ProfileNJ. RefineTree takes a gene tree with statistical supports on its branches, and corrects its weakly supported parts by using a combination of…

JRC…
Dataset

JRC GMO-Amplicons

Contains and makes available results of a bioinformatic pipeline that regularly…

Contains and makes available results of a bioinformatic pipeline that regularly screens public nucleotide sequence databanks. JRC GMO-Amplicons includes patents and available whole plant genomes,…

Hetero-RP
Desktop

Hetero-RP Heterogeneity Rescaling Pursuit

Introduces a scalable algorithm to weight important features tuning-free…

Introduces a scalable algorithm to weight important features tuning-free without tedious cross-validation for tuning parameters. Hetero-RP is a scalable and tuning-free preprocessing framework for…

Pheno4J
Desktop

Pheno4J

Permits fast efficient storage and querying of large volumes of structured…

Permits fast efficient storage and querying of large volumes of structured genetic and phenotypic data. Pheno4J is scalable and respects the number of exomes stored in memory. It allows users to…

GenomeHubs
Dataset

GenomeHubs

Facilitates the setup and hosting of custom Ensembl genome browsers. GenomeHubs…

Facilitates the setup and hosting of custom Ensembl genome browsers. GenomeHubs is based on a containerized approach that allows it to be run on any computer architecture and greatly reduces the time…

PhyDesign
Web

PhyDesign

A platform-independent online application that implements the Townsend…

A platform-independent online application that implements the Townsend phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic…

MyGene.info
Web

MyGene.info

Provides simple-to-use REST web services to query/retrieve gene annotation…

Provides simple-to-use REST web services to query/retrieve gene annotation data. MyGene.info is designed with simplicity and performance emphasized. You can use it to power a web application which…

ALTree
Desktop

ALTree Association and Localisation tests using haplotype phylogenetic Trees

Converts the output of the haplotype reconstruction programs to input for…

Converts the output of the haplotype reconstruction programs to input for phylogeny reconstruction programs. ALTree tests the association between a candidate gene and a disease, and pinpoints markers…

Organism.dply
Desktop

Organism.dply

Provides an alternative interface to Bioconductor 'annotation'…

Provides an alternative interface to Bioconductor 'annotation' resources, in particular the gene identifier mapping functionality of the 'org' packages and the genome coordinate…

org.Hs.eg.db
Desktop

org.Hs.eg.db

Contains mappings between Entrez Gene identifiers and GenBank accession…

Contains mappings between Entrez Gene identifiers and GenBank accession numbers. org.Hs.eg.db is an R object and an organism specific package that provides detailed information about the species…

Rbrother
Desktop

Rbrother

Makes a Bayesian multiple change-point model, one of the most sophisticated…

Makes a Bayesian multiple change-point model, one of the most sophisticated model-based phylogenetic recombination tools. Rbrother detects recombination while accounting for changes both in tree…

CRANN
Desktop

CRANN

Allows investigation of adaptive evolution in a number of ways. CRANN has been…

Allows investigation of adaptive evolution in a number of ways. CRANN has been developed in order to detect adaptive evolution in protein-coding DNA sequences. It checks to ensure that the alignment…

GeneNomenclatur…
Desktop

GeneNomenclatureUtils

Simplifies the comparison of lists of genes produced by different labs.…

Simplifies the comparison of lists of genes produced by different labs. GeneNomenclatureUtils offers means to fetch the key nomenclature and other genomic, bibliographic and disease annotation…

genome_updater
Desktop

genome_updater

Provides an automatic download and update genome and sequences files from NCBI.…

Provides an automatic download and update genome and sequences files from NCBI. genome_updater is a Shell script that keeps log and version for each update.

Metadata…
Desktop

Metadata categorization

Allows expert biological indexers to curate a sample set drawn from NCBI…

Allows expert biological indexers to curate a sample set drawn from NCBI BioSample data. Metadata categorization is a package that identify terms in the user submission that can be correlated to…

Afra
Desktop

Afra

Aims to mutualize the identification of genome sequences’ organisms. Afra…

Aims to mutualize the identification of genome sequences’ organisms. Afra recruits additional gene feature curators to increase the understanding of genomes. The goal of the platform is to increase…

GeneALaCart
Web

GeneALaCart

Generates a file of GeneCards annotations associated with a list of genes.…

Generates a file of GeneCards annotations associated with a list of genes. GeneALaCart is a batch-querying application that provides a powerful method for working with sets of genes. For each query,…

MARE
Desktop

MARE MAtrice REduction

Delivers an alternative heuristics which assesses tree-likeness of partitions…

Delivers an alternative heuristics which assesses tree-likeness of partitions ('genes') in supermatrices using extended geometry mapping. MARE reduces supermatrices with a simple hill…

SECISearch3…
Web

SECISearch3 and Seblastian

Tools for prediction of SECIS elements and selenoproteins.

Tools for prediction of SECIS elements and selenoproteins.

XORRO
Desktop

XORRO

An extremely efficient paired-read overlap program for use with Illumina…

An extremely efficient paired-read overlap program for use with Illumina sequencing.

NHGRI
Nontypeable

NHGRI National Human Genome Research Institute

Establishing a Central Resource of Data from Genome Sequencing Projects.

Establishing a Central Resource of Data from Genome Sequencing Projects.

NHGRI Talking…
Nontypeable

NHGRI Talking Glossary

The National Human Genome Research Institute (NHGRI) created the Talking…

The National Human Genome Research Institute (NHGRI) created the Talking Glossary of Genetic Terms to help everyone understand the terms and concepts used in genetic research.

MSG
Desktop

MSG Multiplexed shotgun genotyping

A pipeline of scripts to assign ancestry to genomic segments using next-gen…

A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data.

Hereditary…
Nontypeable

Hereditary Hearing loss Homepage

Aims to give an up-to-date overview of the genetics of hereditary hearing…

Aims to give an up-to-date overview of the genetics of hereditary hearing impairment for researchers and clinicians working in the field.

CDP
Nontypeable

CDP Cancer Diagnosis Program

Strives to improve the diagnosis and assessment of cancer by effectively moving…

Strives to improve the diagnosis and assessment of cancer by effectively moving new scientific knowledge into clinical practice.

DCTD
Nontypeable

DCTD Division of Cancer Treatment and Diagnosis

Takes prospective detection and treatment leads, facilitates their paths to…

Takes prospective detection and treatment leads, facilitates their paths to clinical application, and expedites the initial and subsequent large-scale testing of new agents, biomarkers, imaging…

EGAPP
Nontypeable

EGAPP Evaluation of Genomic Applications in Practice and Prevention

The Working Group was established to support the development of a systematic…

The Working Group was established to support the development of a systematic process for assessing the available evidence regarding the validity and utility of genetic tests for clinical practice.

Genehopper
Web

Genehopper

A high performant search engine that extends the set of tools to explore human…

A high performant search engine that extends the set of tools to explore human gene-to-gene relationships by a large number of gene similarities and the possibility to combine them into a…

HUMHOT
Dataset

HUMHOT HUman Meiotic Recombination HOt Spots

Stores more than 130 meiotic recombination hot spot sequences identified in…

Stores more than 130 meiotic recombination hot spot sequences identified in humans. HUMHOT gathers for every hot spot sequence various details such as locus name, chromosome number, hot spot sequence…

MeSA
Desktop

MeSA

Smooths the impact of asymmetry or imbalance at a node which is dependent of…

Smooths the impact of asymmetry or imbalance at a node which is dependent of the number of species during a phylogeny analyse. MeSa allows the user to manipulated datasets in sophisticated ways, can…

Recode-2
Dataset

Recode-2

Informs user about genes known to utilize translational recoding. Recode…

Informs user about genes known to utilize translational recoding. Recode permits user to visualize annotated sequence elements, do complex search queries, and browse recoding data.

The Ruby UCSC…
Desktop

The Ruby UCSC API

Allows users to query on the UCSC genome database. The Ruby UCSC API permits to…

Allows users to query on the UCSC genome database. The Ruby UCSC API permits to fetch the database schema of that table to determine the data types and then creates an appropriate Ruby class for that…

The Genome…
Terminology

The Genome Properties database

Gathers definitions for the higher-level attributes which can be ascribed to a…

Gathers definitions for the higher-level attributes which can be ascribed to a species when a sufficient set of molecular markers are detected in its genome, or else reported jointly absent. The…

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