:: DESCRIPTION
EvalDNA uses machine-learning methods to integrate genome assembly quality metrics into a single comprehensive quality score.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MacDonald ML, Lee KH.
EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality.
BMC Bioinformatics. 2021 Nov 27;22(1):570. doi: 10.1186/s12859-021-04480-2. PMID: 34837948.
:: DESCRIPTION
StoatyDive is a tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets. It can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data.
::DEVELOPER
Bioinformatics Group Albert-Ludwigs-University Freiburg
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Heyl F, Backofen R.
StoatyDive: Evaluation and classification of peak profiles for sequencing data.
Gigascience. 2021 Jun 18;10(6):giab045. doi: 10.1093/gigascience/giab045. PMID: 34143874; PMCID: PMC8212874.
:: DESCRIPTION
SCONE (Sequence CONservation Evaluation) reports position-specific measures of conservation.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Analysis of sequence conservation at nucleotide resolution.
Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S.
PLoS Comput Biol. 2007 Dec;3(12):e254. Epub 2007 Nov 14.
:: DESCRIPTION
TSCAN (Tools for Single-Cell ANalysis) is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.
Ji Z, Ji H.
Nucleic Acids Res. 2016 May 13. pii: gkw430.
:: DESCRIPTION
REAPR (Recognising Errors in Assemblies using Paired Reads) is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
REAPR: a universal tool for genome assembly evaluation.
Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD.
Genome Biol. 2013 May 27;14(5):R47
:: DESCRIPTION
STOVCA (STructural OVerlap CAlculator) is a software that takes as input a pairwise structure superposition of proteins, DNA or RNA in PDB format generated by any software and produces a standardized structural alignment and its corresponding similarity measures, according to the parameters provided by the user. Therefore, STOVCA allows the direct comparison and ranking of structural superpositions generated by any structure superposition software
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Jan 1;29(1):47-53. doi: 10.1093/bioinformatics/bts600. Epub 2012 Oct 11.
Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments.
Slater AW1, Castellanos JI, Sippl MJ, Melo F.
:: DESCRIPTION
CAD-score is a new evaluation function quantifying differences between physical contacts in a model and the reference structure.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
CAD-score: A new contact area difference-based function for evaluation of protein structural models.
Olechnovič K, Kulberkytė E, Venclovas C.
Proteins. 2013 Jan;81(1):149-62. doi: 10.1002/prot.24172. Epub 2012 Sep 29.
:: DESCRIPTION
EEEP (Efficient Evaluation of Edit Paths) is a software to infer putative pathways of lateral genetic transfer by comparing gene trees against a rooted reference tree (PL)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Beiko, R.G. and Hamilton, N. (2006).
Phylogenetic identification of lateral genetic transfer events.
BMC Evolutionary Biology 6:15.
:: DESCRIPTION
Dove is a deep learning based protein docking model evluation method.It will use the atom information such as postions, types, energy scores in the interface area to judge if the docking model is reasonable.
::DEVELOPER
Kihara Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2019 Nov 20. pii: btz870. doi: 10.1093/bioinformatics/btz870. [Epub ahead of print]
Protein Docking Model Evaluation by 3D Deep Convolutional Neural Networks.
Wang X, Terashi G, Christoffer CW, Zhu M, Kihara D.
:: DESCRIPTION
MetaReg is a Java application aimed to provide the biologist with an intuitive graphical interface for both definition and analysis of system models. The application makes it possible to navigate the model network and compare its predicted and observed behavior.
::DEVELOPER
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
I. Gat-Viks and R. Shamir.
MetaReg application: a graphical interface for modeling and evaluation of biological systems.
Genome Biology (2008) Vol. 9 No. R1
