CCD 1.0 – Core Collection of Diverse Taxa

CCD 1.0

:: DESCRIPTION

CCD is a Java software package for the selection of core collections of diverse taxa (e.g. from germplasm collections) that are intended to capture the genetic diversity of the input dataset.

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

CCD

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

  CCD

:: MORE INFORMATION

Citation

Davey R, Savva G, Jing R, Lott M, Ellis THN, Ambrose M, Moulton V, Flavell A, Roberts I and Dicks J (2006)
Germplasm collections: Gaining new knowledge from old datasets.
Proceedings of the 2nd UK KDD Conference pp 32-38.

SUPERSMART / supersmartR – Estimating Rates of Speciation and Migration, Ages and Relationships of Taxa

SUPERSMART / supersmartR

:: DESCRIPTION

SUPERSMART is a platform for automated mining of molecular sequences, large-scale phylogenetic inference and fossil calibration.

::DEVELOPER

Antonelli Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux /  MacOsX
  • R

:: DOWNLOAD

supersmartR

:: MORE INFORMATION

Citation

Syst Biol. 2017 Mar 1;66(2):152-166. doi: 10.1093/sysbio/syw066.
Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.
Antonelli A et al.

branchCut 1.0 – Breaks long Branches in a Tree by adding Taxa

branchCut 1.0

:: DESCRIPTION

branchCut takes a phylogenetic tree and break longest branches until a certain number of taxa is reached.

::DEVELOPER

The Computational Phylogenetics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 branchCut

:: MORE INFORMATION

PRUNETREE 5.0 – Trimming Taxa Off Phylogenies

PRUNETREE 5.0

:: DESCRIPTION

Prunetree is a program for trimming taxa off phylogenies. You can make subtrees by either including (or excluding) a specific group of taxa. In addition, it also has options to arbitrarily transform internode branch lengths (BL) following a speciational model (all BL = 1) or following Pagel?s method (all taxa aligned and all internode BL = 1).

::DEVELOPER

The Lajeunesse Lab

:: SCREENSHOTS

PRUNETREE

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PRUNETREE

 :: MORE INFORMATION