OrthoClust – Orthology-based Network Framework for Clustering data across multiple Species

OrthoClust

:: DESCRIPTION

OrthoClust is a clustering algorithm built on a multilayer network framework. It concatenates networks from individual species by their orthology relationships, arriving at a multiplex network. By optimizing the a generalized modularity function, OrthoClust returns a set of modules that could be either conserved or species-specific.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

OrthoClust

:: MORE INFORMATION

Citation:

Genome Biol. 2014 Aug 28;15(8):R100. doi: 10.1186/gb-2014-15-8-r100.
OrthoClust: an orthology-based network framework for clustering data across multiple species.
Yan KK, Wang D, Rozowsky J, Zheng H, Cheng C, Gerstein M.

Phylo-HMRF – Comparing 3D Genome Organization in Multiple Species

Phylo-HMRF

:: DESCRIPTION

Phylo-HMRF (Phylogenetic Hidden Markov Random Field model) identifies evolutionary patterns of 3D genome based on multi-species Hi-C data.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

Phylo-HMRF

:: MORE INFORMATION

Citation

Cell Syst. 2019 Jun 26;8(6):494-505.e14. doi: 10.1016/j.cels.
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.
Yang Y, Zhang Y, Ren B, Dixon JR, Ma J.

OrthoVenn – Comparison and Annotation of Orthologous Gene Clusters among multiple Species

OrthoVenn

:: DESCRIPTION

OrthoVenn is a web platform for comparison and annotation of orthologous gene clusters among multiple species.

::DEVELOPER

OrthoVenn team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.
Wang Y, Coleman-Derr D, Chen G, Gu YQ.
Nucleic Acids Res. 2015 May 11. pii: gkv487.

MultiModule 1.0 – de novo Discovery of Cis-regulatory Modules in Multiple Species

MultiModule 1.0

:: DESCRIPTION

MultiModule: Discovery of cis-regulatory modules in multiple species by coupling hidden Markov models

::DEVELOPER

Qing Zhou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MultiModule

:: MORE INFORMATION

Citation

Zhou, Q. and Wong, W.H. (2007).
Coupling hidden Markov models for the discovery of cis-regulatory modules in multiple species.
The Annals of Applied Statistics, 1: 36-65.