linACC 0.1.4 – Detection of Lineage Specific Accelerated Substitution Rates

linACC 0.1.4

:: DESCRIPTION

linACC exploits a hierarchy of nested evolutionary models to detect lineage specific acceleraton of substitution rates in different species/branches.

::DEVELOPER

Kostka Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R

:: DOWNLOAD

linACC

:: MORE INFORMATION

Citation

Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages.
D Kostka, AK Holloway, KS Pollard
Molecular Biology and Evolution, 35(8):2034-2045 2018.

RateEvolver 1.1 – Simulate Evolution of Substitution Rate on Fixed Nine-taxon Tree

RateEvolver 1.1

:: DESCRIPTION

RateEvolver simulates the evolution of the substitution rate on a fixed nine-taxon tree. It allows the rate to vary among branches in either an autocorrelated or uncorrelated manner.

::DEVELOPER

the Molecular Ecology, Evolution, and Phylogenetics laboratory in the School of Biological Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 RateEvolver

:: MORE INFORMATION

Citation

Ho, S. Y., Phillips, M. J., Drummond, A. J., & Cooper, A. (2005).
Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation.
Molecular Biology and Evolution, 22(5), 1355-1363.

Coevol 1.4b – Correlated Evolution of Substitution Rates and Phenotypes

Coevol 1.4b

:: DESCRIPTION

Coevol is a Bayesian MCMC software for comparative analyses combining molecular data and continuous characters (e.g. ecological variables or life-history traits.)

::DEVELOPER

Nicolas Lartillot (nicolas.lartillot@umontreal.ca)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 Coevol

:: MORE INFORMATION

Citation

Lartillot N, Poujol R.
A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters.
Mol Biol Evol. 2011 Jan;28(1):729-44. Epub 2010 Oct 6.

GZ-gamma – Estimate Parameter of Substitution Rate Variation among Sites

GZ-gamma

:: DESCRIPTION

GZ-gamma is designed to estimate the expected number of substitutions of each amino acid (nucleotide) site, and the gamma shape parameter for the rate variation among sites, using a combination of ancestral sequence inference and maximum likelihood estimation when the phylogenetic relationships of these homologous sequences are known.

::DEVELOPER

Jianzhi Zhang ,  Xun Gu 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  GZ-gamma

:: MORE INFORMATION

Citation:

Gu, X. and J. Zhang J (1997)
A simple method for estimating the parameter of substitution rate variation among sites.
Mol. Biol. Evol. 14:1106-1113