capDSD – Confidence, Augmented Pathway Diffusion State Distance

capDSD

:: DESCRIPTION

capDSD is an extension of DSD that takes in to account a measure of interaction confidence while also incorporating directed pathway data.

::DEVELOPER

Cowen Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Python

:: DOWNLOAD

capDSD

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jun 15;30(12):i219-i227. doi: 10.1093/bioinformatics/btu263.
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence.
Cao M, Pietras CM, Feng X, Doroschak KJ, Schaffner T, Park J, Zhang H, Cowen LJ, Hescott BJ.

GUIDANCE 2.02 – Guide-tree based Alignment Confidence

GUIDANCE 2.02

:: DESCRIPTION

The GUIDANCE web-server is a powerful and user-friendly tool for assigning a confidence score for each residue, column, and sequence in an alignment and for projecting these scores onto the MSA. The server points to columns and sequences that are unreliably aligned and enables their automatic removal from the MSA, in preparation for downstream analyses.

::DEVELOPER

GUIDANCE Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

GUIDANCE

:: MORE INFORMATION

Citation

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.
Sela I, Ashkenazy H, Katoh K, Pupko T.
Nucleic Acids Res. 2015 Apr 16. pii: gkv318.

Penn, O., Privman, E., Ashkenazy, H., Landan, G., Graur, D. and Pupko, T. (2010).
GUIDANCE: a web server for assessing alignment confidence scores.
Nucleic Acids Research, 2010 Jul 1; 38 (Web Server issue):W23-W28; doi: 10.1093/nar/gkq443

Consel 0.20 – Assess Confidence of Phylogenetic Tree Selection

Consel 0.20

:: DESCRIPTION

CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection. CONSEL does not estimate the phylogenetic tree by itself, but CONSEL does read the output of the other phylogenetic packages, such as Molphy, PAML, PAUP*, TREE-PUZZLE, and PhyML. CONSEL calculates the p-value using several testing procedures; the bootstrap probability, the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and the weighted Shimodaira-Hasegawa test. In addition to these conventional tests, CONSEL calculates the p-value based on the approximately unbiased test using the multi-scale bootstrap technique.

::DEVELOPER

Hidetoshi Shimodaira

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows

:: DOWNLOAD

CONSEL

:: MORE INFORMATION

Citation:

Shimodaira, H. & Hasegawa, M.
CONSEL: for assessing the confidence of phylogenetic tree selection.
Bioinformatics 17, 1246-1247 (2001).

CapFilter – Analysis tool for Identifying high Confidence Transcription Start Sites

CapFilter

:: DESCRIPTION

CapFilter is a straightforward annotation-agnostic computational pipeline that greatly increases confidence in predicted TSSs and allows tuning by the end-user to balance both precision and sensitivity of TSS identification to address experimental needs.

::DEVELOPER

Megraw Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CapFilter

:: MORE INFORMATION

Citation

Jason S. Cumbie, Maria G. Ivanchenko, and Molly Megraw. (2015).
NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.
BMC Genomics, 16:597. doi:10.1186/s12864-015-1670-6

Coev2Net – Boosting Confidence in High-throughput Protein-protein Interaction datasets

Coev2Net

:: DESCRIPTION

Coev2Net is a general framework to predict, assess and boost confidence in individual interactions inferred from a HTP experiment. For every pair of interaction in the HTP screen, Coev2Net provides a score to assess their likelihood of being co-evolved from interacting homologous sequences.

::DEVELOPER

Bonnie Berger‘s group at MIT.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Perl

:: DOWNLOAD

Coev2Net

:: MORE INFORMATION

Citation:

Genome Biol. 2012 Aug 31;13(8):R76.
A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.
Hosur R, Peng J, Vinayagam A, Stelzl U, Xu J, Perrimon N, Bienkowska J, Berger B.

CITE 1.0 – Confidence Intervals for Divergence Time Estimates

CITE 1.0

:: DESCRIPTION

CITE computes a Confidence InTerval Estimate from a substitution and a mutation rate.

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Mol Biol Evol. 2001 Jul;18(7):1157-60.
Statistics of divergence times.
Haubold B, Wiehe T.