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Hieranoid / Hierarchical Orthology Inference
Allows orthology inference. Hieranoid is an hybrid between tree and graph based approaches that infer groups of orthologs in a hierarchical structure. The software uses a species tree as a guide tree which reduces the number of proteome comparisons to N-1 for N proteomes. Hieranoid can be parallelized on compute cluster. One of its benefits is its linearly scaling compute time which makes it useful for applications with large multispecies sets of proteomes.
A toolkit that implements an adjusted MCScan algorithm for detection of synteny and collinearity and incorporates 14 computer programs for visualizing and analyzing identified synteny and collinearity. MCScanX scans multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and aligns these regions using genes as anchors. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families.
A web platform for comparison and annotation of orthologous gene clusters among multiple species. OrthoVenn provides comprehensive coverage of vertebrates, metazoa, protists, fungi, plants and bacteria for identify orthologous gene clusters and supports user define species to upload customized protein sequences. It has an efficient and interactive graphic tool which provide a Venn diagram view for comparing two to six species protein sequences. The only thing user need to do is choosing species or upload protein sequences.
BLASTO / BLAST on Orthologous groups
Provides a variation of BLAST tool for detecting orthologous group. BLASTO is a web application that aims to assist users in deducing the function of a sequence and its hypothetic phylogenetic relationships to other sequences through a comparison performed towards various databases. Users can set a wide range of parameters such as genetic codes or substitution matrices and choose between five different databases including NCBI COG, NCBI KOG, OrthoMCL DB, MultiParanoid and TIGR EGO.
A software system incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species. OrthoInspector is a database of precomputed orthology and inparalogy relationships and a stand-alone package allowing large-scale predictions of orthology between thousands of proteomes. The resource provides improved speed, esay installation in a network environment, visualisation tools and the possibility to built complex queries based on phylogenetic profiles.
OrthoMaM / Orthologous Mammalian Markers
A database of orthologous mammalian markers describing the evolutionary dynamics of orthologous genes in mammalian genomes using a phylogenetic framework. Since its first release in 2007, OrthoMaM has regularly evolved, not only to include newly available genomes but also to incorporate up-to-date software in its analytic pipeline. OrthoMaM has proven to be a valuable resource for researchers interested in mammalian phylogenomics, evolutionary genomics, and has served as a source of benchmark empirical data sets in several methodological studies.
DLRSOrthology / Duplication Loss Rate and Sequence Orthology
A package to compute orthology probabilities. DLRSOrthology enables orthology inference with respect to the DLRS (Duplication, Loss, Rate and Sequence) model by extending the original PrIME-DLR framework with new algorithms, and comes in two variants: the variable-tree variant and fixed-tree variant. DLRSOrthology outperforms competing approaches on synthetic data as well as on biological data sets and is robust to incomplete taxon sampling artifacts.
BUSCO / Benchmarking Universal Single-Copy Orthologs
Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. BUSCO assessments are implemented in open-source software, with comprehensive lineage-specific sets of benchmarking universal single-copy orthologs for arthropods, vertebrates, metazoans, fungi, eukaryotes, and bacteria.
A method for hierarchical clustering of homology relations and identification of orthologous groups of genes. Unlike previous approaches, which are based on pairwise sequence comparisons, this method explores the correlation of evolutionary histories of individual genes in a more global context. COCO-CL can be used as a semi-independent method to delineate the orthology/paralogy relation for a refined set of homologous proteins obtained using a less-conservative clustering approach, or as a refiner that removes putative out-paralogs from clusters computed using a more inclusive approach.
ORCAN / ORtholog sCANner
A web-based meta-server for one-click evolutionary and functional annotation of protein sequences. ORCAN combines information from the most popular orthology-prediction resources, including 4 tools and 4 online databases. Functional annotation utilizes 5 additional comparisons between the query and identified homologs, including: sequence similarity, protein domain architectures, functional motifs, Gene Ontology term assignments, and a list of associated articles. Furthermore, the server uses a plurality-based rating system to evaluate the orthology relationships and to rank the reference proteins by their evolutionary and functional relevance to the query.
HOMECAT / HOmology Mapper for Enrichment and Comparative Analysis with Translation
Allows cross-species data comparison with a particular emphasis on functional genomic data (i.e. microarrays and other high throughput biological data sources). HOMECAT aims to facilitate cross-species relationship identification and data mapping, by combining orthology predictions from several publicly available sources, a convenient interface for high-throughput data download and automatic identifier conversion into a Cytoscape plug-in, that provides both an integration with a large set of bioinformatics tools, as well as a user-friendly interface.
Predicts the reaction of a plant type III polyketide synthases (PKS). pPAP targets PKSs acting on ring-type starter substrates, and classifies their functions into four reaction types. It is based on linear discriminant analyses of similarity measures. The tool can detect distant paralogs of the R-4- A type. It combines two measures: one calculated by profile hidden Markov models (pHMMs) built from functionally and structurally important partial sequence regions, and the other based on mutual information between residue positions.
An improved system for one-to-one ortholog assignment. For a pair of input genomes, the system first focuses on the tandemly duplicated genes of each genome and tries to identify among them those that were duplicated after the speciation (i.e., the so-called inparalogs), using a simple phylogenetic tree reconciliation method. For each such set of tandemly duplicated inparalogs, all but one gene will be deleted from the concerned genome (because they cannot possibly appear in any one-to-one ortholog pairs), and MSOAR is invoked.
Identifies ortholog groups among multiple genomes. MultiMSOAR provides information about gene births, duplications and losses in evolution, which may be of independent biological interest. It is able to infer evolutionary events much more accurately than a well-known software tool Notung. The tool was compared to MultiParanoid and shows significantly higher prediction accuracy. It outperforms MultiParanoid, the Roundup multi-ortholog repository and the Ensembl ortholog database in real data experiments using gene symbols as a validation tool.
eggNOG-mapper / Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups mapper
Allows fast functional annotation of novel sequences. eggNOG-mapper can annotate collections of sequences, typically targeting translated gene-coding regions from genomes, metagenomes, and transcriptomics data. It provides three steps: sequence mapping, orthology assignment and functional annotation. This tool is based on a collection of Hidden Markov Models (HMMs) available into the eggNOG database.
WORMHOLE / WORM Human OrthoLogy Explorer
Applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. WORMHOLE intelligently incorporates predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. A web tool allows users to rapidly query the WORMHOLE database for LDO predictions between the six species, including options to manually define the WORMHOLE score threshold, exclude all but the highest scoring predicted LDOs for genes with multiple mappings, and select only WORMHOLE RBHs. Genome-wide ortholog predictions between each pair of species are also available for download.
Helps is the construction of ortholog data sets for phylogenetic analysis. Ortholog-Finder is a program to eliminate the effects of horizontal gene transfer (HGT) genes and out-paralogs from the ortholog data set. It includes five processes: HGT filtering, out-paralog filtering, classification of tree data, tree splitting, and E-value changing. To obtain orthologs, Ortholog-Finder requires two known groups of species, because the program identifies and removes out-paralogs based on the phylogenetic tree constructed with a root.
HaMStR / Hidden Markov Model based Search for Orthologs using Reciprocity
Extends predefined groups of orthologous genes derived from taxa. HaMStR exhibits a very low false positive rate (FDR) and good sensitivity. For it, a profile Hidden Markov Model (HMM) that captures the essential features of the known orthologs is used in the ortholog search. This tool is able to compile informative data sets for contemporary phylogenomic studies and to standardize data acquisition for studies in molecular systematics.
SearchDOGS / Searches against a Database of Orthologous Genomic Segments
Detects missing genes in annotated bacterial genomes. SearchDOGS uses conserved local synteny across species combined with BLASTX sequence similarity searches to identify genes. It was developed to be applicable to any set of suitable species where extensive local synteny can be established. For each species in the input set, this method generates a list of automatic predictions based on sequence similarity and conserved genomic location.
DIOPT / Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool
Allows rapid identification of orthologs. DIOPT integrates existing approaches, facilitating rapid identification of orthologs among human, mouse, zebrafish, C. elegans, Drosophila, and S. cerevisiae. DIOPT graphical user interface (GUI) allows researchers with different goals to appropriately 'cast a wide net' or limit results to highest confidence predictions. DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. This helps users to identify the most appropriate matches among multiple possible orthologs.
DIOPT-DIST / DIOPT Diseases and Traits
Maps gene-disease relationships from the NCBI Online Mendelian Inheritance in Man (OMIM) database and genome-wide association studies (GWAS) datasets contained in the GWAS catalog to genes in the C. elegans, Drosophila, mouse, S. cerevisiae, and zebrafish genomes using DIOPT orthologous predictions. DIOPT-DIST allows users to search the related human diseases by a list of genes from model organisms or the corresponding genes in model organisms by disease term, disease category or IDs from OMIM. Both gene/locus OMIM IDs and disease phenotype OMIM IDs can be searched at DIOPT-DIST.
LmCGST / Listeria monocytogenes Core-Genome Sequence Typer
Provides increased discriminatory power relative to typing methods such as pulsed-field gel electrophoresis, ribotyping, and multi-locus sequence typing while it addresses several shortcomings of other methods of molecular characterization with next-generation sequence data. LmCGST can analyze raw reads, identify an organism’s HCC profile, compare that profile to an expandable database, provide an evolutionarily meaningful sequence type assignment and generate a phylogenetic analysis that illustrates the evolutionary relationship of the subject to the members of the database.
Improves the specificity of ortholog identification and is suitable for high-throughput use. Ortholuge provides important data set evaluation for a variety of analyses based on comparative approaches, including gene function prediction, prediction of conserved regulatory elements, and comparative analysis of gene order or gene/protein expression data. It will aid those performing various comparative genomics-based analyses, such as the prediction of conserved regulatory elements upstream of orthologous genes.
Processes clustered expressed sequence tags (EST) sequences automatically for phylogenomic studies. OrthoSelect carries out analyses on a phylogenomic scale. It integrates publicly available bioinformatic tools and manages data processing and storage. It also automates the construction of data sets for phylogenomic studies, so user can evaluate intermediate results at any time of the analysis. This pipeline produces automatically calculated and post-processed alignments that can be used as input for common phylogenetic reconstruction software.
PSAT / Prokaryotic Sequence homology Analysis Tool
Allows users to perform comparative genomics tasks. PSAT authorizes to compare a single reference genome with the bacterial genomes publicly available through NCBI, including selected genomes from the Burkholderia, Escherichia, Francisella, Salmonella, Pseudomonas, and Yersinia genera. The software provides a graphic representation of genomic neighborhoods and highlights the related regions for its homologs. Besides, a downloadable local version makes it possible to run personalized analysis.
Identifies orthologous (and paralogous) nucleotide or amino acid sequences, which resolves existing algorithmic and software-technical issues. Orthograph applies a best reciprocal hit search strategy using profile hidden Markov models and maps nucleotide sequences to the globally best matching cluster of orthologous genes, thus enabling researchers to conveniently and reliably delineate orthologs and paralogs from transcriptomic and genomic sequence data. It is easy to install and use and thereby facilitates comparative analyses of transcriptomic and other coding sequence data.
NemaFootPrinter / Nematode Transcription Factor Scan Through Philogenetic Footprinting
Assists researchers in the identification of conserved non-coding sequence regions between the genomes of the two nematodes C. elegans and C. briggsae. NemaFootPrinter is a web application that proceeds to the identification of conserved functional segments outside exons (putative new gene expression control elements) through comparative genomics. Moreover, the investigator can retrieve the genome DNA sequences of the two orthologous genes, visualize graphically the genes' intron/exon structure and the surrounding DNA regions.
DeNoGAP / De-Novo Genome Analysis Pipeline
Performs reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis. DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of Genomes. It scales linearly since the homology assignment is based on iteratively refined hidden Markov models. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences.
BiDiBlast / Bi-Directional BLAST
An approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. BiDiBlast submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. It enables the average user with an ordinary personal computer to perform the matching of two sets of sequences by means of a bi-directional, BLAST or TBLASTX search. The resulting of local alignment matches can be complemented by a subsequent global alignment in order to evaluate each hit properly.
Wheat Zapper
A fast and flexible on-line application to predict orthologous relationships with the model species Oryza sativa, Brachypodium dystachyon, and Sorghum bicolor. Wheat Zapper was specifically designed to provide plant scientists with a set of tools, comprising not only synteny inference, but also automated primer design, intron/exon boundaries prediction, visual representation using the graphic tool Circos 0.53, and the possibility of downloading FASTA sequences for downstream applications. Quality of the "Wheat Zapper" prediction was confirmed against the genome of maize, with good correlation (r > 0.83) observed between the gene order predicted on the basis of synteny and their actual position on the genome.
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Collects homologue from diverse animal genomes. aLeaves collects sequences similar to an input query sequence from various data sources. It provides a unique online platform to explore metazoan gene family trees on demand. The database includes genome project-based datasets covering 100 metazoan species, as well as sequences from the widely used public database GenBank. It only includes species with sequenced and published genomes whose gene annotation is already made publicly accessible.
POGs2 / Putative Orthologous Groups 2
Brings together functional and structural annotations for orthologous genes in a manner that simplifies cross-species comparison and functional inference. POGs2 is a database that retains the user-friendly single-page view and flexible search strategies of the original POGsDB. It offers flexible and intuitive options for queries based on gene identifier, keywords, domain names, InterPro domain identifiers, and predicted or established intracellular locations.
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