CEpBrowser 20150219 – Comparison of Epigenomic Modifications across Species

CEpBrowser 20150219

:: DESCRIPTION

CEpBrowser (Comparative Epigenome Browser) is a gene-centric genome browser that visualize the genomic features of multiple species with color-coded orthologous regions, aiding users in comparative genomic research. The genome browser is adapted from UCSC Genome Browser and the orthologous regions are generated from cross-species lift-over pairs.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 1;29(9):1223-5. doi: 10.1093/bioinformatics/btt114. Epub 2013 Mar 29.
Enabling interspecies epigenomic comparison with CEpBrowser.
Cao X, Zhong S.

HiDe 20120609 – Infer Highways of Horizontal Gene Transfer in the Evolutionary History of a set of Species

HiDe 20120609

:: DESCRIPTION

HiDe (short for Highway Detection) is a software package for inferring highways of horizontal gene transfer in the evolutionary history of a set of species. HiDe takes as input a collection of unrooted gene trees along with a rooted species tree.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 HiDe 

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Mar 1;29(5):571-9. doi: 10.1093/bioinformatics/btt021. Epub 2013 Jan 17.
Systematic inference of highways of horizontal gene transfer in prokaryotes.
Bansal MS, Banay G, Harlow TJ, Gogarten JP, Shamir R.

SpeciesGeoCoder 1.1.0 / speciesgeocodeR 2.0-10- Coding of Species into user-defined units

SpeciesGeoCoder 1.1.0 / speciesgeocodeR 2.0-10

:: DESCRIPTION

SpeciesGeoCoder is a free software package for coding species occurrences into user-defined units for e.g. biogeographic analyses. using a combination of GIS polygons and altitudinal ranges.

speciesgeocodeR is an R-package for the preparation for geographic point occurrence data in biogeographic analyses.

::DEVELOPER

Antonelli Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux /  MacOsX
  • R / Python

:: DOWNLOAD

SpeciesGeoCoder / speciesgeocodeR

:: MORE INFORMATION

Citation

SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.
Töpel M, Zizka A, Calió MF, Scharn R, Silvestro D, Antonelli A.
Syst Biol. 2017 Mar 1;66(2):145-151. doi: 10.1093/sysbio/syw064.

Sampbias – Sampling Bias in Species Distribution Records

Sampbias

:: DESCRIPTION

Sampbias is a method and tool to 1) visualize the distribution of occurrence records and species in any user-provided dataset, 2) quantify the biasing effect of geographic features related to human accessibility, such as proximity to cities, rivers or roads, and 3) create publication-level graphs of these biasing effects in space.

::DEVELOPER

Antonelli Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux /  MacOsX
  • R

:: DOWNLOAD

Sampbias

:: MORE INFORMATION

GSP – Genome Specific Primers Design in Polyploid Species

GSP

:: DESCRIPTION

GSP is a web-based platform to design genome-specific primers that distinguish subgenome sequences in a polyploid genome.

::DEVELOPER

GSP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GSP

:: MORE INFORMATION

Citation

GSP: a web-based platform for designing genome-specific primers in polyploids.
Wang Y, Tiwari VK, Rawat N, Gill BS, Huo N, You FM, Coleman-Derr D, Gu YQ.
Bioinformatics. 2016 Mar 9. pii: btw134.

tfbs_species 1.0 – Map Human Transcription Factor Binding Sites to Another Species

tfbs_species 1.0

:: DESCRIPTION

The aim of tfbs_species is to translate a list of binding sites from the University of California Santa Cruz(UCSC) Genome database from one species to another. At the moment, this data only exists for the human genome

::DEVELOPER

Raymond Wan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

  tfbs_species

:: MORE INFORMATION

MultiOrigin 1.0 – Exploring Hypotheses about the number of origins and the time of origin of a species founded by discrete events

MultiOrigin 1.0

:: DESCRIPTION

MultiOrigin explores hypotheses about the number of origins and time of origin of species that are founded from an ancestral species through discrete events (i.e. polyploid species). The program uses a population divergence coalescence model together with a rejection sampling algorithm.

::DEVELOPER

Jakobsson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/ Windows 

:: DOWNLOAD

  MultiOrigin

:: MORE INFORMATION

Citation

Jakobsson et al. (2006)
A Unique Recent Origin of the Allotetraploid Species Arabidopsis suecica: Evidence from Nuclear DNA Markers
Mol. Biol. Evol. 23: 1217-1231,

Indicspecies 1.7.5 – Studying the Statistical Relationship between Species and groups of sites

Indicspecies 1.7.5

:: DESCRIPTION

Indicspecies‘ is an R package that contains a set of functions to assess the strength of relationship between species and a classification of sites.

::DEVELOPER

Miquel De Cáceres Ainsa

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Windows / Linux
  • R package

:: DOWNLOAD

 Indicspecies

:: MORE INFORMATION

Citation

Improving indicator species analysis by combining groups of sites
Miquel De Cáceres, Pierre Legendre, Marco Moretti
Oikos Volume 119, Issue 10, pages 1674–1684, October 2010

MUGBAS 20150313 – Species free Gene-based Programme Suite for Post-GWAS Analysis

MUGBAS 20150313

:: DESCRIPTION

MUGBAS (MUlti species Gene-Based Association Suite) is a open source pipeline for obtaining gene based results from a given GWA study.

::DEVELOPER

MUGBAS team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/MacOsX
  • R
  • Perl
  • Python

:: DOWNLOAD

 MUGBAS

:: MORE INFORMATION

Citation:

MUGBAS: a species free gene-based programme suite for post-GWAS analysis.
Capomaccio S, Milanesi M, Bomba L, Vajana E, Ajmone Marsan P.
Bioinformatics. 2015 Mar 11. pii: btv144.

HomoVert 0.4.1 – Convert Entrez Gene IDs from one Species to another

HomoVert 0.4.1

:: DESCRIPTION

HomoVert is a package to convert Entrez Gene IDs from one species to another.  It has a builtin Homologene conversion table and a function to convert your Gene IDs to a second species of your choice.  Also outputs gene symbol, protein ID and protein accession numbers.

::DEVELOPER

Fero Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HomoVert

:: MORE INFORMATION