• OrthoMCL

  • Referenced in 15 articles [sw29602]
  • OrthoMCL: identification of ortholog groups for eukaryotic genomes. The identification of orthologous groups is useful ... OrthoMCL provides a scalable method for constructing orthologous groups across multiple eukaryotic taxa, using ... Markov Cluster algorithm to group (putative) orthologs and paralogs. This method performs similarly ... genomes, but can be extended to cluster orthologs from multiple species. OrthoMCL clusters are coherent...
  • IsoRank

  • Referenced in 13 articles [sw08324]
  • human. The global alignment immediately suggests functional orthologs across these species; we believe these ... first set of functional orthologs that cover all the five species. We show that these ... functional orthologs compare favorably with current sequence-only orthology prediction approaches, including better prediction ... orthologs for some human disease-related proteins...
  • SMART

  • Referenced in 16 articles [sw17187]
  • databases, and integrates these with predictions of orthology. New visualization tools have been developed ... these displays to provide schematic comparisons of orthologous genes, or multiple transcripts from the same...
  • eggNOG

  • Referenced in 11 articles [sw17022]
  • eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral ... sequences. A database of orthologous groups and functional annotation...
  • Proteinortho

  • Referenced in 9 articles [sw29601]
  • Proteinortho: Detection of co-orthologs in large-scale analysis. Proteinortho is a tool to detect ... orthologous genes within different species. For doing so, it compares similarities of given gene sequences ... additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (manuscript in preparation...
  • PhyME

  • Referenced in 9 articles [sw35645]
  • algorithm for finding motifs in sets of orthologous sequences. Background: This paper addresses the problem ... more genes, as well as their orthologs in other species. Results: We propose an algorithm ... probabilistic score. The algorithm allows the input orthologous sequences to be related by any user...
  • MSOAR

  • Referenced in 7 articles [sw29658]
  • MSOAR: a high-throughput ortholog assignment system based on genome rearrangement. - MSOAR 2.0: Incorporating tandem ... duplications into ortholog assignment based on genome rearrangement. Background: Ortholog assignment is a critical ... fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different ... throughput system for assigning one-to-one orthologs between closely related species on a genome...
  • OrthoDB

  • Referenced in 5 articles [sw22979]
  • update of the hierarchical catalog of orthologs and the underlying free software. Orthology, refining ... increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about ... update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including ... uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups...
  • PathBLAST

  • Referenced in 9 articles [sw29737]
  • first path are paired with putative orthologs occurring in the same order in the second...
  • STITCH

  • Referenced in 6 articles [sw17006]
  • transferring interactions between species to rely on orthology rather than protein similarity. This improves ... where scores are now transferred only to orthologous proteins, but not to paralogous proteins. STITCH...
  • OMA

  • Referenced in 3 articles [sw34207]
  • Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical ... orthologous group inference. Results: We present improvements in the OMA algorithm: (i) refining the pairwise ... orthology inference step to account for same-species paralogs evolving at different rates ... minimizing errors in the pairwise orthology verification step by testing the consistency of pairwise distance...
  • TOPD/FMTS

  • Referenced in 6 articles [sw19992]
  • comparison of trees that contain both orthologs and paralogs. Each option is also complemented with...
  • OrthoGNC

  • Referenced in 2 articles [sw34205]
  • OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation. Orthology relations ... gene (or protein) to another. Hence, detecting orthology relations has become an important task ... gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood ... used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software...
  • QuartetS

  • Referenced in 2 articles [sw34206]
  • fast and accurate algorithm for large-scale orthology detection. The unparalleled growth in the availability ... data offers both a challenge to develop orthology detection methods that are simultaneously accurate ... high throughput and an opportunity to improve orthology detection by leveraging evolutionary evidence ... sequenced genomes. Here, we report a novel orthology detection method, termed QuartetS, that exploits evolutionary...
  • PlantTFDB

  • Referenced in 4 articles [sw17023]
  • RefSeq, STRING and Entrez Gene. By inferring orthologous groups and constructing phylogenetic trees, evolutionary relationships...
  • GIGA

  • Referenced in 4 articles [sw29606]
  • gene trees as being composed of orthologous subtrees (containing only speciation events), which are joined...
  • CONREAL

  • Referenced in 2 articles [sw18497]
  • transcription factor binding sites. The use of orthologous sequences and phylogenetic footprinting approaches have become ... AVID-based predictions of conserved TFBSs in orthologous promoters. Comparative analysis using different algorithms...
  • PrimAlign

  • Referenced in 2 articles [sw34148]
  • approaches are based on the notion that orthologous proteins across species are sequentially similar ... that topology of PPIs between orthologs is often conserved. However, high accuracy and scalability...
  • HUMAnN

  • Referenced in 1 article [sw13868]
  • summaries as outputs: The abundance of each orthologous gene family in the community. Orthologous families ... same biological roles. HUMAnN uses the KEGG Orthology (KO) by default, but any catalog ... orthologs can be employed with minor changes (COG, NOG, etc.) The presence/absence of each pathway...
  • Mercator

  • Referenced in 1 article [sw23116]
  • Mercator: Multiple Whole-Genome Orthology Map Construction. Whole-genome homology maps attempt to identify ... thus we will use the terms ”homologous”, ”orthologous”, and ”paralogous” instead. Ideally, given K genomes ... would like to identify all orthologous genomic regions as well as paralogous regions within each ... form a program called Mercator that constructs orthology maps between multiple whole genomes...