HaMStR 13.2.6 – Hidden Markov Model based Search for Orthologs using Reciprocit

HaMStR 13.2.6

:: DESCRIPTION

HaMStR (Hidden Markov Model based Search for Orthologs using Reciprocity)is a Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HaMStR

:: MORE INFORMATION

Citation:

BMC Evol Biol. 2009 Jul 8;9:157.
HaMStR: profile hidden markov model based search for orthologs in ESTs.
Ebersberger I, Strauss S, von Haeseler A.

inGeno 0.6 – Integrated Genome and Ortholog Viewer

inGeno 0.6

:: DESCRIPTION

inGeno is designed for genome sequence comparisons, which has been proven to be powerful, in particular to prokaryotic genomes of close phylogenetic distances. The original purpose of this software is to user-friendly visualize the corresponding relationships between orthologous genes. Step by step, a series of algorithms are implemented and integrated together, thus enable a noise-reducing process, a locus collinear block recognition and a text-mining step, which are helpful for users to extract biological information precisely.

::DEVELOPER

Department of BioinformaticsBiocenterUniversity of Würzburg, Germany

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 inGeno

:: MORE INFORMATION

Citation

inGeno–an integrated genome and ortholog viewer for improved genome to genome comparisons.
Liang C, Dandekar T.
BMC Bioinformatics. 2006 Oct 20;7:461.

LOFT 1.0.5 – Orthology Prediction at Scalable Resolution by Phylogenetic Tree analysis

LOFT 1.0.5

:: DESCRIPTION

LOFT (Levels of Orthology From Trees) assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large) trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable.

::DEVELOPER

the Centre for Molecular and Biomolecular Informatics,the CMBI.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  LOFT

:: MORE INFORMATION

Citation

René TJM van der Heijden,
Orthology prediction at scalable resolution by phylogenetic tree analysis,
BMC Bioinformatics 2007, 8:83

BUSCO v1.1b1 – Assessing Genome Assembly and Annotation Completeness with Single-copy Orthologs

BUSCO v1.1b1

:: DESCRIPTION

BUSCO completeness assessment employs sets of Benchmarking Universal Single-Copy Orthologs from OrthoDB to provide quantitative measures of the completeness of genome assemblies, annotated gene sets, and transcriptomes in terms of expected gene content.

::DEVELOPER

Zdobnov’s Computational Evolutionary Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • NCBI BLAST+
  • HMMER (HMMER 3.1b2)
  • Augustus 3.0.x

:: DOWNLOAD

 BUSCO

:: MORE INFORMATION

Citation

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM.
Bioinformatics. 2015 Jun 9. pii: btv351.

DODO – DOmain based Detection of Orthologs

DODO

:: DESCRIPTION

DODO is an efficient method to detect orthologs in genomes. Given protein sequences of interested genomes, DODO can identify orthologous relationship based on protein domain information.

::DEVELOPER

Transcriptome Discovery Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DODO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S6. doi: 10.1186/1471-2105-11-S7-S6.
DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection.
Chen TW1, Wu TH, Ng WV, Lin WC.

SPOCS 1.0.10 – Graph-based Ortholog/Paralog Prediction tool

SPOCS 1.0.10

:: DESCRIPTION

SPOCS (Species Paralogy and Orthology Clique Solver) is a graph-based ortholog/paralog prediction tool that will predict orthologs and paralogs given a set of prokaryotic proteomes (the set of proteins encoded by a genome). The software will take a set of protein fasta files (one per species genome), and an optional additional fasta to serve as an outgroup (a species that should be more distantly related to the species of interest than any of the species of interest are to each other).

::DEVELOPER

Computational Biology & Bioinformatics ,Pacific Northwest National Laboratory

:: SCREENSHOTS

SPOCS

:: REQUIREMENTS

  • Linux/ MacOsX
  • C++ Compiler
  • NCBI BLAST

:: DOWNLOAD

 SPOCS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 15;29(20):2641-2. doi: 10.1093/bioinformatics/btt454.
SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.
Curtis DS, Phillips AR, Callister SJ, Conlan S, McCue LA.

OrthoNets 1.0 – Simultaneous Visual Analysis of Orthologs and their Interaction Neighborhoods across different organisms

OrthoNets 1.0

:: DESCRIPTION

OrthoNets provides various information about the proteins and interactions – including domain architectures (bottom of figure 1), protein and gene aliases, pubmed identifiers of the publications supporting the interactions, and the experiment type used to detect the interaction. Here the view is focused on the RNA polymerase enzyme LEO1 – so that only the LEO1 node and its recorded interaction partners are displayed.

::DEVELOPER

The Wodak Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 OrthoNets

:: MORE INFORMATION

Citation

Yanqi Hao, Anna Merkovitch, James Vlasblom, Shuye Pu, Andrei L. Turinsky, Denitza Roudeva, Brian Turner, Jack Greenblatt, Shoshana J. Wodak.
OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.
Bioinformatics. 2011 Mar 15;27(6):883-4. Epub 2011 Jan 20.

POPE – Phylogeny, Ortholog and Paralog Extractor

POPE

:: DESCRIPTION

POPE is a tool to aid high-throughput phylogenetic analysis.POPE provides an integrated platform for automatic ortholog identification. Intermediate steps can be visualized, modified and analyzed in order to assess and improve the underlying quality of orthology and paralogy assignments.

::DEVELOPER

Thorhildur Juliusdottir

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  POPE

:: MORE INFORMATION

Citation:

Bioinformatics. 2008 Dec 1;24(23):2778-9. Epub 2008 Oct 10.
POPE–a tool to aid high-throughput phylogenetic analysis.
Juliusdottir T, Pettersson F, Copley RR.

Gene-warp 3.2 – Generate Alignment Matrices, Explore Temporal Asynchrony in Expression of Orthologs

Gene-warp 3.2

:: DESCRIPTION

Gene-warp is a tool to select ortholog pairs with best alignments and to explore alignment paths (not expression profiles!) shared by many genes. The program takes as an input two related datasets, containing profiles of orthologous genes.

::DEVELOPER

Dmitri Papatsenko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  Gene-warp

:: MORE INFORMATION

Citation

Goltsev Y, Papatsenko D.
Time warping of evolutionary distant temporal gene expression data based on noise suppression
BMC Bioinformatics. 2009 Oct 26;10:353.

THOR 1.0 – Assemble Target Genomic Sequence Orthologs

THOR 1.0

:: DESCRIPTION

THOR (Targeted High-throughput Ortholog Reconstructor) is a Java application designed to assemble target genomic sequence orthologs in low-coverage genomes.

::DEVELOPER

Kevin Teague

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 THOR

:: MORE INFORMATION

Citation

Matthew N. Bainbridge* René L. Warren, An He, Mikhail Bilenky, A. Gordon Robertson and Steven J.M. Jones
THOR: targeted high-throughput ortholog reconstructor
Bioinformatics (2007) 23 (19): 2622-2624