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.

deBGA – de Bruijn Graph-based Aligner

deBGA

:: DESCRIPTION

deBGA is a seed-and-extension-based read alignment tool. It is suitable for aligning various kinds of high-throughput sequencing reads to multiple similar reference genomes.

::DEVELOPER

HIT Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C Compiler

:: DOWNLOAD

 deBGA

:: MORE INFORMATION

Citation:

deBGA: read alignment with de Bruijn Graph-based seed and extension.
Liu B, Guo H, Brudno M, Wang Y.
Bioinformatics. 2016 Jul 4. pii: btw371.