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.

TOPD/FMTS 4.6 – Comparing Phylogenetic Trees

TOPD/FMTS 4.6

:: DESCRIPTION

TOPD/FMTS  (TOPological Distance / From Multiple To Single)is a new software for comparing phylogenetic trees. It has been developed to calculate the differences between trees.

::DEVELOPER

P. Puigbo, Ph.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • tcl/tk
  • Perl

:: DOWNLOAD

 TOPD/FMTS

:: MORE INFORMATION

Citation

Puigbo P., Garcia-Vallve S. and McInerney J.O. (2007)
TOPD/FMTS: a new software to compare phylogenetic trees.
Bioinformatics, 23:1556-1558. doi: 10.1093/bioinformatics/btm135.

CompPhy – A Web-based Collaborative Platform for comparing Phylogenies

CompPhy

:: DESCRIPTION

CompPhy is a web platform dedicated to the collaborative handling of phylogenetic trees.

:: DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Evol Biol. 2014 Dec 14;14(1):253.
CompPhy: a web-based collaborative platform for comparing phylogenies.
Fiorini N, Lefort V, Chevenet F, Berry V, Chifolleau AM.

Amordad 1.0 – Database Engine for comparing Metagenomic data

Amordad 1.0

:: DESCRIPTION

Amordad is a database engine for comparing metagenomic data at massive scale. It first obtains the sequence signature of metagenomes and organizes them as points in high dimensional space.

::DEVELOPER

The Smith Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Amordad

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 27. pii: btu405. [Epub ahead of print]
The Amordad database engine for metagenomics.
Behnam E, Smith AD.

CSM-lig – A Web Server for Assessing and Comparing Protein-small molecule Affinities

CSM-lig

:: DESCRIPTION

CSM-lig is a web server tailored to predict the binding affinity of a protein-small molecule complex based on structural signatures.

::DEVELOPER

CSM-lig team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CSM-lig: a web server for assessing and comparing protein-small molecule affinities.
Pires DE, Ascher DB.
Nucleic Acids Res. 2016 May 5. pii: gkw390.

gffcompare 0.9.6f – Comparing, Annotating, Merging and Tracking Transcripts in GFF files

gffcompare 0.9.6f

:: DESCRIPTION

gffcompare is a program for comparing, annotating, merging and tracking transcripts in GFF(General Feature Format) files

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 gffcompare

:: MORE INFORMATION

GeneNomenclatureUtils – Tools for Annotating Genes and Comparing Gene Lists with Community Resources

GeneNomenclatureUtils

:: DESCRIPTION

GeneNomenclatureUtils is a command-line utilities for using MGI, Entrez, HGNC, PubMed, and OMIM files.

::DEVELOPER

Genes to Cognition (G2C)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GeneNomenclatureUtils

:: MORE INFORMATION

modelBorgifier 1.0 – Comparing and Merging Metabolic Models

modelBorgifier 1.0

:: DESCRIPTION

Matching and comparison of genome-scale reconstructions and models are facilitated by modelBorgifier. It reconciles models in light of different annotation schemes, allowing diverse models to become useful for synchronous investigation.

::DEVELOPER

BRAIN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MATLAB
  • COBRA Toolbox

:: DOWNLOAD

 modelBorgifier

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):1036-8. doi: 10.1093/bioinformatics/btt747. Epub 2013 Dec 25.
Assimilating genome-scale metabolic reconstructions with modelBorgifier.
Sauls JT1, Buescher JM.

Surface Diver – Comparing, and Classifying Proteins according to their Physicochemical Properties

Surface Diver

:: DESCRIPTION

Surface Diver allows describing, comparing, and classifying proteins according to their physicochemical properties without the need of prior 3D structural alignment.

::DEVELOPER

Biomolecular Machines Laboratory 

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Surface Diver

:: MORE INFORMATION

Citation

Maciej Dlugosz, Joanna Trylska
Electrostatic similarity of proteins: Application of 3D spherical harmonic decomposition,
J. Chem. Phys., 129:015103, 2008

ResProx – Comparing the overall Quality of NMR Protein Structures

ResProx

:: DESCRIPTION

ResProx (Resolution-by-proxy or Res(p)) is a web server that predicts the atomic resolution of NMR protein structures using only PDB coordinate data as input.

::DEVELOPER

Wishart Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • VMware

:: DOWNLOAD

  ResProx

:: MORE INFORMATION

Citation

Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.
Berjanskii M, Zhou J, Liang Y, Lin G, Wishart DS.
J Biomol NMR. 2012 Jul;53(3):167-80. doi: 10.1007/s10858-012-9637-2