Mercator 2013.01.11 – Multiple Whole-Genome Orthology Map Construction

Mercator 2013.01.11

:: DESCRIPTION

MERCATOR is an orthology mapping program suitable for multiple genomes.Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term “syntenic” is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an ancestral genome. However, it has been pointed out that this use of the term is incorrect (Passarge et al. 1999) and thus we will use the terms “homologous”, “orthologous”, and “paralogous” instead. Ideally, given K genomes, we would like to identify all orthologous genomic regions as well as paralogous regions within each genome and hypothetical ancestral genome. Maps listing these relationships are extremely valuable to researchers performing comparative analyses of genomic sequence.

::DEVELOPER

Colin DeweyPachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Mercator

:: MORE INFORMATION

Citation

Colin N. Dewey, Peter M. Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter
Parametric Alignment of Drosophila Genomes
PLoS Comput Biol 2(6): e73. doi:10.1371/journal.pcbi.0020073

ERA v1 – Efficient Serial and Parallel Suffix Tree Construction

ERA v1

:: DESCRIPTION

ERA (Elastic Range), a disk-based suffix tree construction method, which works efficiently with very long strings that are much larger than the available memory.

::DEVELOPER

InfoCloud Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C Compiler

:: DOWNLOAD

 ERA

:: MORE INFORMATION

Citation:

Essam Mansour, Amin Allam, Spiros Skiadopoulos, Panos Kalnis:
ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings.
PVLDB 5(1): 49-60 (2011)

Faucet v0.5 – Streaming de novo Assembly Graph Construction

Faucet v0.5

:: DESCRIPTION

Faucet is an streaming metagenome assembler. It uses low memory and disk space and achieves highly contiguous assemblies.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Faucet

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Jan 1;34(1):147-154. doi: 10.1093/bioinformatics/btx471.
Faucet: streaming de novo assembly graph construction.
Rozov R, Goldshlager G, Halperin E, Shamir R.

DendroUPGMA 201410 – A Dendrogram Construction Utility

DendroUPGMA 201410

:: DESCRIPTION

Use DendroUPGMA to create a dendrogram from (a) a set of variables, (b) a similarity matrix or (c) a distance matrix. The program calculates a similarity matrix (only for option a), transforms similarity coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm.

::DEVELOPER

P. Puigbo, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

S. Garcia-Vallve, J. Palau and A. Romeu (1999)
Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis.
Molecular Biology and Evolution 9:1125-1134.

SaffronTree v0.1.2 – Reference Free Rapid Phylogenetic Tree Construction from raw read data

SaffronTree v0.1.2

:: DESCRIPTION

SaffronTree takes FASTQ/FASTA files as input and uses a kmer analysis to build a phylogenetic neighbour joining tree in newick format.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SaffronTree

:: MORE INFORMATION

Gen3D – 3D Genome and Chromosome Structural Model Construction

Gen3D

:: DESCRIPTION

Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations.

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 Gen3D

:: MORE INFORMATION

Citation

Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data.
Nowotny J, Ahmed S, Xu L, Oluwadare O, Chen H, Hensley N, Trieu T, Cao R, Cheng J.
BMC Bioinformatics. 2015 Oct 23;16(1):338.

HighMap – Construction and Analysis of High-density Linkage Map

HighMap

:: DESCRIPTION

HighMap software is suitable for genetic map. This software utilized maximum likelihood and smooth algorithm, and could deal with ten thousand markers that make map distance more stably.

::DEVELOPER

Biomarker Technologies Corporation

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Construction and analysis of high-density linkage map using high-throughput sequencing data.
Liu D, Ma C, Hong W, Huang L, Liu M, Liu H, Zeng H, Deng D, Xin H, Song J, Xu C, Sun X, Hou X, Wang X, Zheng H.
PLoS One. 2014 Jun 6;9(6):e98855. doi: 10.1371/journal.pone.0098855.

stringgaussnet 1.1 – PPI and Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor

stringgaussnet 1.1

:: DESCRIPTION

stringgaussnet is a toolbox for a construction of protein-protein interaction networks through the ‘STRING’ application programming interface, and an inference of Gaussian networks through ‘SIMoNe’ and ‘WGCNA’ approach, from DE genes analysis results and expression data. Additional functions are provided to import automatically networks into an active ‘Cytoscape’ session.

::DEVELOPER

Emmanuel Chaplais <emmanuel.chaplais at inserm.fr>, Henri-Jean Garchon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • R

:: DOWNLOAD

 stringgaussnet

:: MORE INFORMATION

Citation

stringgaussnet: from differentially expressed genes to semantic and gaussian networks generation.
Chaplais E, Garchon HJ.
Bioinformatics. 2015 Jul 30. pii: btv450.

Tripal 2.0 – Construction of online Genetic and Genomic databases

Tripal 2.0

:: DESCRIPTION

Tripal is a collection of open-source freely available Drupal modules and is a member of the GMOD family of tools. Tripal serves as a web interface for the GMOD Chado database and is designed to allow anyone with genomic data to quickly create an online genomic database using community supported tools.

::DEVELOPER

Tripal team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • PHP
  • phpPgAdmin
  • MySQL or PostgreSQL
  • Chado

:: DOWNLOAD

 Tripal

:: MORE INFORMATION

Citation

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases.
Sanderson LA, Ficklin SP, Cheng CH, Jung S, Feltus FA, Bett KE, Main D.
Database (Oxford). 2013 Oct 25;2013:bat075. doi: 10.1093/database/bat075.

MC-NET 1.0 – Construction of Phylogenetic Networks

MC-NET 1.0

:: DESCRIPTION

MC-Net is A method for the construction of phylogenetic networks based on Monte-Carlo method

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

 MC-NET

:: MORE INFORMATION

Citation

BMC Evol Biol. 2010 Aug 20;10:254. doi: 10.1186/1471-2148-10-254.
MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method.
Eslahchi C1, Habibi M, Hassanzadeh R, Mottaghi E.