:: DESCRIPTION
GenCo is program to estimate gene conversion and crossover rates in population genetic data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gay J, Myers S, and McVean G (2007).
Estimating meiotic gene conversion rates from population genetic data.
Genetics 177:881-94.
:: DESCRIPTION
PEDEL (Programme for Estimating Diversity in Error-prone PCR Libraries) can be used to calculate the expected number of distinct variants present in a library, given the library size, mean substitution rate and parent sequence length. On the web page, the user may produce plots of the expected number of distinct daughter sequences as a function of library size and substitution rate.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
AndrewE. Firth, Wayne M. Patrick, 2005,
Statistics of protein library construction,
Bioinformatics, 21, 3314-3315.
:: DESCRIPTION
TIMER estimates the divergence times using linearized-tree approach. Compared with the program LINTREE (Takezaki et al. 1995), TIMER has more user-friendly interface. More importantly, TIMER can be used to estmate divergence times for concatenated or very large set of genes (proteins).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Glazko, G. V. and M. Nei (2003)
Estimation of divergence times for major lineages of primate species.
Mol. Biol. Evol. 20:424-434.
:: DESCRIPTION
PoooL is a novel constrained EM algorithm to estimate frequencies of single-nucleotide polymorphism (SNP) haplotypes from DNA pools. A quantity called importance factor is introduced to measure the contribution of a haplotype to the likelihood. Under the assumption of asymptotic normality of the estimated allele frequencies and a system of linear constraints on haplotype frequencies the importance factor remains a constant in the iterative maximization process.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Han Zhang, Hsin-Chou Yang and Yaning Yang
PoooL: An efficient algorithm for estimating haplotype frequencies from large DNA pools
Bioinformatics 2008 24(17):1942-1948
:: DESCRIPTION
ArrayOme is a new software system to predict the size of the microarray-visualised genome (MVG) based on microarray-derived comparative genomic hybridization data.
::DEVELOPER
Hong-Yu Ou (tjohy@hotmail.com)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hong-Yu Ou et al.
ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes
Nucl. Acids Res. (2005) 33 (1): e3.
:: DESCRIPTION
codonbias will allow the user to estimate selection coefficients relating to optimal codon usage. The basic methodology is similar to the codon based models implemented in the popular program PAML by Ziheng Yang. However, it explicitly models selection for optimal codon usage on different lineages of a phylogeny.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
HGT is a software to simulate and estimate Horizontal Gene Transfer events.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Simone Linz, Achim Radtke, Arndt von Haeseler
A Likelihood Framework to Measure Horizontal Gene Transfer
Molecular Biology and Evolution, 24:1312-1319, 2007.
:: DESCRIPTION
Mykiss is a computer program for estimating the reproductive success of individuals based on genetic data (codominant genotypes).
::DEVELOPER
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ML-NullFreq estimates the Frequency of Null Alleles at Microsatellite Loci.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Steven T Kalinowski, Mark L Taper
Maximum likelihood estimation of the frequency of null alleles at microsatellite loci
Conservation Genetics (2006) Volume: 7, Issue: Pages: 991-995
:: DESCRIPTION
COB is a parsimony-based method of computing likelihoods accurately under the coalescent with recombination.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lyngsø, R., Song, Y.S., and Hein, J.
Accurate computation of likelihoods in the coalescent with recombination via parsimony.
Lect Notes Comput Sci. 2008; 4955(LNBI): 463–477.
