FRST 1.2 – Protein Model Quality Estimation Method

FRST 1.2

:: DESCRIPTION

FRST serves to validate the energy of a protein structure. The server computes both an overall and a per-residue energy profile of a protein structure. The energy profile can be visualized in different ways, including a per-residue plot and a colored structure representation, accessible as a series of dynamic web pages.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FRST

:: MORE INFORMATION

Citation:

Silvio C.E. Tosatto.
The Victor/FRST Function for Model Quality Estimation.
Journal of Computational Biology 2005; 12(10):1316-1327

FUGUE 0.2.3 – Haplotype Frequency Estimation

FUGUE 0.2.3

:: DESCRIPTION

FUGUE is the program used to construct haplotypes for the chromosome and linkage disequilibrium maps.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • MERLIN

:: DOWNLOAD

FUGUE

:: MORE INFORMATION

Citation:

Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR and Dunham I
A first-generation linkage disequilibrium map of human chromosome
Nature (2002) 418:544-548

Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, Ankener WM, Alfisi SV, Kuo FS, Camisa AL, Pazorov V, Scott KE, Carey BJ, Faith J, Katari G, Bhatti HA, Cyr JM, Derohannessian V, Elosua C, Forman AM, Grecco NM, Hock CR, Kuebler JM, Lathrop JA, Mockler MA, Nachtman EP, Restine SL, Varde SA, Hozza MJ, Gelfand CA, Broxholme J, Abecasis GR, Boyce-Jacino MT and Cardon LR
Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots.
Nat Genet (2003) 33:382-7

SLR 1.4.3 – Sitewise Likehood Ratio Estimation of Selection

SLR 1.4.3

:: DESCRIPTION

SLR (Sitewise Likehood Ratio) is a program to detect sites in coding DNA that are unusually conserved and/or unusually variable (that is, evolving under purify or positive selection) by analysing the pattern of changes for an alignment of sequences on an evolutionary tree. The strength of selection at each site is determined by comparing the rate of nonsynonymous (amino acid changing) substitutions to that of synonymous (silent) substituions, the latter assumed to be invisible to selection and so evolving in a strictly neutral fashion.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 SLR

:: MORE INFORMATION

Citation:

Genetics. 2005 Mar;169(3):1753-62. Epub 2005 Jan 16.
Detecting amino acid sites under positive selection and purifying selection.
Massingham T, Goldman N.

cn.FARMS 1.34.0 – Factor Analysis for Copy Number Estimation

cn.FARMS 1.34.0

:: DESCRIPTION

cn.FARMS is a latent variable model for detecting copy number variations in microarray data.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R Package
  • BioConductor

:: DOWNLOAD

 cn.FARMS

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(12):e79. doi: 10.1093/nar/gkr197. Epub 2011 Apr 12.
cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate.
Clevert DA1, Mitterecker A, Mayr A, Klambauer G, Tuefferd M, De Bondt A, Talloen W, G?hlmann H, Hochreiter S.

MetaPIGA v3.1 – Large Phylogeny Estimation

MetaPIGA v3.1

:: DESCRIPTION

MetaPIGA is a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a random-restart hill climbing, a simulated annealing algorithm, a classical genetic algorithm, and the metapopulation genetic algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data.

::DEVELOPER

Laboratory of Artificial & Natural Evolution

:: SCREENSHOTS

MetaPIGA

:: REQUIREMENTS

  • MacOsX / Linux / Windows
  • Java

:: DOWNLOAD

  MetaPIGA

:: MORE INFORMATION

Citation

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics
aphaël Helaers & Michel C. Milinkovitch
BMC Bioinformatics 2010, 11:379

Ribomap v1.2 – Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abudance

Ribomap v1.2

:: DESCRIPTION

Ribomap is a package that generates isoform-level ribosome profiles from ribosome profiling data.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • Sailfish/Salmon

:: DOWNLOAD

Ribomap

:: MORE INFORMATION

Citation

Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
Wang H, McManus J, Kingsford C.
Bioinformatics. 2016 Jun 15;32(12):1880-2. doi: 10.1093/bioinformatics/btw085

Facet v1.4 – Multiple Alignment Accuracy Estimation and Parameter Advising

Facet v1.4

:: DESCRIPTION

Facet (Feature-based accuracy estimator) computes a single estimate of accuracy as a linear combination of efficiently-computable feature functions.

::DEVELOPER

Dr. Dan DeBlasio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

Facet

:: 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.

STEM 2.0 / STEM-hy 1.0 – Species Tree Estimation using Maximum likelihood (with hybridization)

STEM 2.0 / STEM-hy 1.0

:: DESCRIPTION

STEM-hy is a program for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 STEM / STEM-hy

:: 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

BEESEM – Binding Energy Estimation on SELEX with Expectation Maximization

BEESEM

:: 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

  • Linux
  • Python

:: DOWNLOAD

BEESEM

:: 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

ReMixT v0.5.4 – Clone-specific Genomic Structure Estimation in Cancer

ReMixT v0.5.4

:: DESCRIPTION

ReMixT is a tool for joint inference of clone specific segment and breakpoint copy number in whole genome sequencing data. The input for the tool is a set of segments, a set of breakpoints predicted from the sequencing data, and normal and tumour bam files. Where multiple tumour samples are available, they can be analyzed jointly for additional benefit.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

ReMixT

:: MORE INFORMATION

Citation

ReMixT: clone-specific genomic structure estimation in cancer.
McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-C?té A, Aparicio S, Sahinalp SC, Shah SP.
Genome Biol. 2017 Jul 27;18(1):140. doi: 10.1186/s13059-017-1267-2.