Pool-hmm 1.4.2 – Estimating Allele Frequencies and Detecting Selective Sweeps

Pool-hmm 1.4.2

:: DESCRIPTION

Pool-hmm aims at estimating allele frequencies and detecting selective sweeps, using NGS data from a sample of pooled individuals from the same population.

::DEVELOPER

Pool-hmm Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Python

:: DOWNLOAD

Pool-hmm

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2013 Mar;13(2):337-40. doi: 10.1111/1755-0998.12063.
Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples.
Boitard S, Kofler R, Fran?oise P, Robelin D, Schl?tterer C, Futschik A.

CatchAll 4.0 – Estimating the Number of Species

CatchAll 4.0

:: DESCRIPTION

CatchAll is a new, platform-independent, user-friendly, computationally optimized software package which calculates a powerful and flexible suite of parametric models (based on current statistical research) in addition to all existing nonparametric procedures.

::DEVELOPER

The Comai Lab

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows
excel

:: DOWNLOAD

CatchAll

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2011:121-30.
Estimating the number of species with CatchAll.
Bunge J.

INPower 0.0.1 – Estimating the number of Susceptibility SNPs and Power of Future studies

INPower 0.0.1

:: DESCRIPTION

IN.power is an R package for estimating the number of susceptibility SNPs and power of future studies.

::DEVELOPER

DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
R package

:: DOWNLOAD

IN.power

:: MORE INFORMATION

Citation

Park J-H, Wacholder S, Gail M, Peters U, Jacobs K, Chanock S, Chatterjee N.
Estimation of effect size distribution from genome-wide association studies and implications for future discoveries.
Nature Genetics, 2010, 42, pp.570-575.

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.

NucDivAFLP – Estimating Nucleotide Diversity from AFLP data

NucDivAFLP

:: DESCRIPTION

NucDivAFLP is a program to estimate nucleotide diversity from AFLP data

::DEVELOPER

the INNAN Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
C Compiler

:: DOWNLOAD

NucDivAFLP

:: MORE INFORMATION

Citation

A method for estimating nucleotide diversity from AFLP data.
Innan H, Terauchi R, Kahl G, Tajima F.
Genetics. 1999 Mar;151(3):1157-64.

ALL-P – Including shared Peptides for Estimating Protein Abundances

ALL-P

:: DESCRIPTION

ALL-P is a statistical framework based on a hierarchical modeling that takes into account shared peptide information for estimating protein abundances. ALL-P performs a simultaneous analysis of all the quantified peptides, handling the biological and technical errors as well as the peptide effect.

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ MacOsX / Linux
R package

:: DOWNLOAD

ALL-P

:: MORE INFORMATION

Citation

Blein-Nicolas M., Xu H., de Vienne D., Giraud C., Huet S., Zivy, M. (2012)
Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics.
Proteomics.12 2797–2801 .

AHLC – Adhockeries for Estimating Divergence Times between Species

AHLC

:: DESCRIPTION

AHLC (ad hoc local clocks) is a software of adhockeries for estimating divergence times between species.

::DEVELOPER

The Aris-Brosou lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

AHLC

:: MORE INFORMATION

Citaion

Aris-Brosou, S. 2007.
Dating phylogenies with hybrid local molecular clocks.
PLoS ONE. 2(9):e879. doi:10.1371/journal.pone.0000879