Tag: Estimator

RUNTC – Estimator of First Coalescent Time

RUNTC

:: DESCRIPTION

RUNTC is an estimator of first coalescent time, which is the time when a copy of a gene most recently shared ancestry with other copies of that gene. This is also an estimate of the upper bound of when a mutation has arisen, and it can be used to study the ages of alleles that are found in a population.

::DEVELOPER

the Hey lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

RUNTC

:: MORE INFORMATION

Citation:

Platt A, Pivirotto A, Knoblauch J, Hey J.
An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations.
PLoS Genet. 2019 Aug 19;15(8):e1008340. doi: 10.1371/journal.pgen.1008340. PMID: 31425500; PMCID: PMC6715256.

ALFRED-G – Distance Estimator for Phylogenetic Inference

ALFRED-G

:: DESCRIPTION

ALFRED-G is an Alignment Free Distance Estimator software for Phylogenetic Inference. It takes as input a set of n sequences and ouputs an n x n matrix of distance estimate for use in Phylogenetic inference.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ALFRED-G

:: MORE INFORMATION

Citation

Thankachan SV, Chockalingam SP, Liu Y, Krishnan A, Aluru S.
A greedy alignment-free distance estimator for phylogenetic inference.
BMC Bioinformatics. 2017 Jun 7;18(Suppl 8):238. doi: 10.1186/s12859-017-1658-0. PMID: 28617225; PMCID: PMC5471951.

Jane – Journal / Author Name Estimator

Jane

:: DESCRIPTION

Just enter the title and/or abstract of the paper in the box, and click on ‘Find journals’ or ‘Find authors’. Jane will then compare your document to millions of documents in Medline to find the best matching journals or authors.

::DEVELOPER

the Biosemantics Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Mar 1;24(5):727-8. doi: 10.1093/bioinformatics/btn006. Epub 2008 Jan 28.
Jane: suggesting journals, finding experts.
Schuemie MJ, Kors JA.

GCE 1.0 – Genomic Character Estimator

GCE 1.0

:: DESCRIPTION

GCE is a bayes model based method to estimate the genome size ,genomic repeat content and the heterozygsis rate of the sequencing sample. The estimated result can be used to design the sequencing strategy.

::DEVELOPER

Binghang Liu (liubinghang@genomics.cn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GCE

:: MORE INFORMATION

Citation

Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects
Binghang Liu, Yujian Shi, Jianying Yuan, Xuesong Hu, Hao Zhang, Nan Li, Zhenyu Li, Yanxiang Chen, Desheng Mu, Wei Fan
arXiv:1308.2012

MareyMap 1.3.4 – Recombination Rate Estimator

MareyMap 1.3.4

:: DESCRIPTION

MareyMap is a meiotic recombination rate estimation program. It is based on R and features a graphical interfcace in tcl/tk. MareyMap comes with an extensive dataset and several interpolation methods. The user may also use MareyMap with his own data.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MareyMap

:: MORE INFORMATION

Citation

Rezvoy, C., Charif, D., Gueguen, L., Marais, G.A.B. (2007)
MareyMap: A R-based tool with graphical interface for estimating recombination rate.
Bioinformatics 23: 2188-2189.”

GraPPLE – Graph Property based Predictor and Likelihood Estimator

GraPPLE

:: DESCRIPTION

GraPPLE are abstract representations of relationships between entities. Through a set of instructions, they are able to convert relationships into nodes and edges. GraPPLE (originally: The RNA sorting hat) leverages the information available from graph properties and the predictive power of support vector machines (SVMs) to classify potential RNA sequences as functional/non-functional and into 1 of 46 Rfam families. In short, GraPPLE predicts the potential function of an ncRNA sequence.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 May;37(9):e66. Epub 2009 Apr 1.
Identification and classification of ncRNA molecules using graph properties.
Childs L, Nikoloski Z, May P, Walther D.

AmpliCoNE – Ampliconic Copy Number Estimator

AmpliCoNE

:: DESCRIPTION

AmpliCoNE is a tool to estimate the copy number of ampliconic gene families in human Y chromosome using Illumina whole genome sequencing data.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

AmpliCoNE

:: MORE INFORMATION

Citation

PLoS Genet, 15 (9), e1008369 2019 Sep 16 eCollection Sep 2019
Dosage Regulation, and Variation in Gene Expression and Copy Number of Human Y Chromosome Ampliconic Genes
Rahulsimham Vegesna , Marta Tomaszkiewicz, Paul Medvedev, Kateryna D Makova

ALE 20180904 – Assembly Likelihood Estimator

ALE 20180904

:: DESCRIPTION

ALE is a probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. It allows for the rapid discovery of errors and comparisons between similar assemblies.

::DEVELOPER

Scott Clark@Cornell University Center for Applied Mathematics, Rob Egan@Department of Energy Joint Genome Institute

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • C Compiler
  • Python

:: DOWNLOAD

 ALE

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):435-43. doi: 10.1093/bioinformatics/bts723. Epub 2013 Jan 9.
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.
Clark SC, Egan R, Frazier PI, Wang Z.

F-Seq 1.84 – Feature Density Estimator for High-Throughput Sequence Tags

F-Seq 1.84

:: DESCRIPTION

F-Seq is a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

::DEVELOPER

Furey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

 F-Seq

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Nov 1;24(21):2537-8. doi: 10.1093/bioinformatics/btn480. Epub 2008 Sep 10.
F-Seq: a feature density estimator for high-throughput sequence tags.
Boyle AP, Guinney J, Crawford GE, Furey TS.

RASER 2.0 – The RAte Shift EstimatoR

RASER 2.0

:: DESCRIPTION

RASER is a likelihood based method for testing and detecting site-specific evolutionary rate shifts.
Given a multiple sequence alignment (MSA) and a phylogenetic tree, the program determines:
(a) Whether or not site-specific rate shifts characterize the evolution of a protein, and
(b) If so, points to the specific sites and lineages in which these shifts have most likely occurred.

::DEVELOPER

 Osnat Penn & Adi Stern

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 RASER

:: MORE INFORMATION

Citation

Penn O, Stern A, Rubinstein ND, Dutheil J, Bacharach E, Galtier N., Pupko T. 2008.
Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes.
PLoS Computational Biology 4(11): e1000214.

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