chromEvol 2.0 – Analyze Changes in Chromosome-number along a Phylogeny

chromEvol 2.0

:: DESCRIPTION

 chromEvol is a program for analyzing changes in chromosome-number along a phylogeny and for the inference of polyploidy.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

   chromEvol

:: MORE INFORMATION

Citation

Mayrose I, Barker MS, Otto SP. 2010.
Probabilistic models of chromosome number evolution and the inference of polyploidy.
Systematic Biology. 59(2):132-144

Cocos – Reconstructing Phylogenies of Multi-Domain Proteins

Cocos

:: DESCRIPTION

Cocos is a tool to construct phylogenies of multi-domain proteins.

::DEVELOPER

Research Group Microbial Virulence

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 Cocos

:: MORE INFORMATION

Citation

Cocos: Constructing multi-domain protein phylogenies.
Homilius M, Wiedenhoeft J, Thieme S, Standfuß C, Kel I, Krause R.
PLoS Curr. 2011 Jun 9;3:RRN1240. doi: 10.1371/currents.RRN1240.

TreePar 3.3 – Estimating Birth and Death Rates based on Phylogenies

TreePar 3.3

:: DESCRIPTION

TreePar is an R package for inferring speciation and extinction rates based on phylogenetic trees.

::DEVELOPER

Computational Evolution group at ETH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • R package

:: DOWNLOAD

 TreePar

:: MORE INFORMATION

Citation

Stadler, T,
Mammalian phylogeny reveals recent diversification rate shifts,
Proc. Nat. Acad. Sci. (2011) 108:6187-6192.

UnderlyingApproach – Alignment-Free Phylogeny of Whole Genomes using Underlying Subwords

UnderlyingApproach

:: DESCRIPTION

The Underlying Approach (UA) builds a scoring function based on this set of patterns, called underlying. This set is by construction linear in the size of input, without overlaps, and can be efficiently constructed. Results show the validity of our method in the reconstruction of phylogenetic trees, where the Underlying Approach outperforms the current state of the art methods. Moreover, the accuracy of UA is achieved with a very small number of subwords, which in some cases carry meaningful biological information.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 UnderlyingApproach

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2012 Dec 6;7(1):34. doi: 10.1186/1748-7188-7-34.
Alignment-free phylogeny of whole genomes using underlying subwords.
Comin M, Verzotto D.

barphlye – Bayesian Rearrangement Phylogeny in Yersinia

barphlye

:: DESCRIPTION

barphlye supplements the BADGER software to analyze patterns present in ancient genome arrangements.

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • R

:: DOWNLOAD

barphlye

:: MORE INFORMATION

Citation

PLoS Genet, 4 (7), e1000128 2008 Jul 18
Dynamics of Genome Rearrangement in Bacterial Populations
Aaron E Darling , István Miklós, Mark A Ragan

RaPPer – Generate Random perfect Phylogeny Matrix

RaPPer

:: DESCRIPTION

RaPPer will generate random perfect phylogeny matrix with following conditions.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Adv Appl Bioinform Chem. 2010;3:89-96. doi: 10.2147/AABC.S13397. Epub 2010 Nov 16.
Construction of random perfect phylogeny matrix.
Sadeghi M1, Pezeshk H, Eslahchi C, Ahmadian S, Abadi SM.

PASSML / Passml_TM – Analysis of Phylogeny / Transmembrane Domain searching from Aligned Amino Acid Sequences

PASSML / Passml_TM

:: DESCRIPTION

PASSML (‘Phylogeny and Secondary Structure using Maximum Likelihood’) has been developed to implement an evolutionary model that combines protein secondary structure and amino acid replacement.

Passml_TM implement an evolutionary model that permits analysis of phylogeny and transmembrane domain searching from aligned amino acid sequences.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PASSML / Passml_TM

:: MORE INFORMATION

Citation

Bioinformatics. 1998;14(8):726-33.
PASSML: combining evolutionary inference and protein secondary structure prediction.
Liò P, Goldman N, Thorne JL, Jones3 DT.

Phy2HTML 1.0 – Display Phylogeny using only HTML and CSS

Phy2HTML 1.0

:: DESCRIPTION

Phy2HTML is a simple Python program that is designed to read a tree in Newick format and create a visualization of the tree for display in a webpage using only HTML and CSS.

::DEVELOPER

Michael S. Rosenberg’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

Phy2HTML

:: MORE INFORMATION

Seq-Gen 1.3.4 – Simulate the Evolution of Sequences along a Phylogeny

Seq-Gen 1.3.4

:: DESCRIPTION

Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Seq-Gen

:: MORE INFORMATION

Citation

Comput Appl Biosci. 1997 Jun;13(3):235-8.
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.
Rambaut A1, Grassly NC.