Tag: species

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,

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

est2assembly 1.13 – Assembly and Annotation of Transcriptomes for any Species

est2assembly 1.13

:: DESCRIPTION

The est2assembly platform is the only platform for standardising transcriptome projects: go from raw trace files to an annotated GBrowse interface driven by the Seqfeature database. It accepts both Sanger and 454 sequencing technology for a denovo assembly, annotation and data mining of EST data.

::DEVELOPER

Dr Alexie Papanicolaou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 est2assembly

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Dec 24;10:447. doi: 10.1186/1471-2105-10-447.
Next generation transcriptomes for next generation genomes using est2assembly.
Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG.

PicoInversionMiner – Detect Pico-inversions between a pair of Species

PicoInversionMiner

:: DESCRIPTION

PicoInversionMiner is a software tool to detect pico-inplace-inversions between closely related species.

::DEVELOPER

Minmei Hou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PicoInversionMiner

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Dec 1;27(23):3266-75. doi: 10.1093/bioinformatics/btr566. Epub 2011 Oct 12.
Pico-inplace-inversions between human and chimpanzee.
Hou M, Yao P, Antonou A, Johns MA.

Synteny – Investigate Sequence Conservation between Species

Synteny

:: DESCRIPTION

Synteny is a tool to investigate sequence conservation between species.

::DEVELOPER

Krawetz Lab

:: SCREENSHOTS

Synteny

:: REQUIREMENTS

  • Windows 

:: DOWNLOAD

 Synteny

:: MORE INFORMATION

Citation

Martins R. P., Krawetz S. A.
Nuclear organization of the protamine locus. Reproduction in Domestic Ruminants,
VI, J. L. Juengel, J. F. Murray, M. F. Smith. Nottingham University Press, NottinghamUK 2007b; 1-12.

Agene – Automatic Generation of Species Specific Gene Predictors

Agene

:: DESCRIPTION

Agene automatically generates a species-specific gene predictor from a set of reliable mRNA sequences and a genome.Author applies a Hidden Markov model (HMM) that implements explicit length distribution modelling for all gene structure blocks using acyclic discrete phase type distributions. The state structure of the each HMM is generated dynamically from an array of sub-models to include only gene features represented in the training set.

::DEVELOPER

Kasper Munch @ The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Agene

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2006 May 21;7:263.
Automatic generation of gene finders for eukaryotic species.
Munch K, Krogh A.

PCI 1.0 – Calculate Barcode Gap Probability of Correct Identification of Species.

PCI 1.0

:: DESCRIPTION

PCI calculates the barcode gap probability of correct identification (PCI) of species.

::DEVELOPER

Statistical Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Perl

:: DOWNLOAD

 PCI

:: MORE INFORMATION

Citation

N. Suwannasai, M.P. Martín, C. Phosri, P. Sihanonth, A.J.S. Whalley and J.L. Spouge
“Fungi in Thailand: A Case Study of the Efficacy of an ITS Barcode for Automatically Identifying Species within the Annulohypoxylon and Hypoxylon Genera”
PLoS One. 2013;8(2):e54529.