:: DESCRIPTION
Facet (Feature-based accuracy estimator) computes a single estimate of accuracy as a linear combination of efficiently-computable feature functions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Comput Biol. 2013 Apr;20(4):259-79. doi: 10.1089/cmb.2013.0007. Epub 2013 Mar 14.
Accuracy estimation and parameter advising for protein multiple sequence alignment.
Kececioglu J, DeBlasio D.
:: DESCRIPTION
STEM-hy is a program for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kubatko, L., B. C. Carstens, and L. L. Knowles. 2009.
STEM: Species Tree Estimation using Maximum likelihood for gene trees under coalescence,
Bioinformatics (2009) 25 (7): 971-973.doi: 10.1093/bioinformatics/btp079
:: DESCRIPTION
The BEESEM program is designed for transcription factor binding motif discovery using HT-SELEX data.
::DEVELOPER
Stormo Lab in Department of Genetics, Washington University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2017 Aug 1;33(15):2288-2295. doi: 10.1093/bioinformatics/btx191.
BEESEM: estimation of binding energy models using HT-SELEX data.
Ruan S, Swamidass SJ, Stormo GD
:: DESCRIPTION
TM (Threshold Model) is a (Fortran90) software for multiple trait estimation of variance components, breeding values and fixed effects in threshold, linear and censored linear models in animal breeding. As of August, 2011 it has been modified to accept random seeds on input, and also to include user-defined covariance matrices among individuals (for instance, genomic relationship matrices).
::DEVELOPER
Andrés Legarra , andres dot legarra at toulouse point inra punto fr
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PMLE estimates the gene flow parameter q for a collection of two or more semi-isolated populations by (pseudo) maximum likelihood using either single or multi locus, haploid or diploid, genotype data. Suitable molecular data types minimally include allozymes, microsatellites, and RFLPs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rannala, B., and J. A. Hartigan. 1996.
Estimating gene flow in island populations.
Genetical Research 67:147-158
:: DESCRIPTION
BACTFREQ estimates allele frequencies and perform the Monte Carlo simulations (replaces BFREQ program)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
E. C. Anderson and P. A. Scheet. 2001.
Improving the estimation of bacterial allele frequencies.
Genetics 158:1383-1386.
B. Rannala, W. Qui, and D. E. Dykhuizen. 2000.
Methods for estimating gene frequencies and detecting selection in bacterial populations
Genetics 155: 499-508.
:: DESCRIPTION
pim is a program for efficiently estimating the number of mismatches between a pair of unaligned sequences
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
B. Haubold, F. A. Reed, and P. Pfaffelhuber.
Alignment-free estimation of nucleotide diversity.
Bioinformatics, doi: 10.1093/bioinformatics/btq689, 2010.
:: DESCRIPTION
CHROMIBD computes IBD probabilities between a “target chromosome” and a set of “parental chromosomes” (the method works best without “phantom parental chromosomes”). These chromosomes need to be phased and the program relies only on phased (non-missing) markers in target and parental chromosomes. The program works only with bi-allelic markers such as SNPs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
T. Druet and F. Farnir (2011)
Modeling of identity-bydescent processes along a chromosome between haplotypes and their genotyped ancestors.
Genetics. 2011 June; 188(2): 409–419.
:: DESCRIPTION
PSCN segments the genome of a sample into homogeneous parts and gives an estimation of parent-specific DNA copy number using high-density SNP array data (logR and B-allele frequency). This package can be applied on platforms having both SNP probes and copy number probes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chen, H., Xing, H. and Zhang, N.R., 2011,
Stochastic segmentation models for allele-specific copy number estimation with SNP-array data,
PLoS Computational Biology, 7, e1001060.
:: DESCRIPTION
BN-BS is a software to estimate branch lengths in terms of synonymous and nonsynonymous substitutions per site, while the tree topology is given. The program uses the modified Nei-Gojobori method (Zhang et al. 1998) to estimate pairwise synonymous and nonsynonymous distances among present-sequences and then estimates branch lengths and their variances by using the ordinary least-squares method.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Zhang J., H. F. Rosenberg, and M. Nei (1998)
Positive Darwinian selection after gene duplication in primate ribonuclease genes.
Proc. Natl. Acad. Sci. USA 95:3708-3713.
