Tag: Inference

MrBayes 3.2.7a – Bayesian Inference of Phylogeny

MrBayes 3.2.7a

:: DESCRIPTION

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes’s theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

::DEVELOPER

MrBayes Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

MrBayes

:: MORE INFORMATION

Citation:

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP.
Syst Biol. 2012 May;61(3):539-42. doi: 10.1093/sysbio/sys029.

Ronquist F, Huelsenbeck JP.
MrBayes 3: Bayesian phylogenetic inference under mixed models.
Bioinformatics. 2003 Aug 12;19(12):1572-4.

GeneRax 1.0.0 – Maximum Likelihood based Gene Tree Inference

GeneRax 1.0.0

:: DESCRIPTION

GeneRax is a tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

GeneRax

:: MORE INFORMATION

Citation

Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis, Gergely Szöllősi.
GeneRax: A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss.
bioRxiv, 779066, 2019

RAxML 8.2.12 / RAxML-NG 0.9.0- Sequential and Parallel Maximum Likelihood based inference of large phylogenetic trees

RAxML 8.2.12 / RAxML-NG 0.9.0

:: DESCRIPTION

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.

RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. RAxML-NG is a successor of RAxML (Stamatakis 2014) and leverages the highly optimized likelihood computation implemented in libpll (Flouri et al. 2014).

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  RAxML , RAxML-NG

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Nov 1;35(21):4453-4455. doi: 10.1093/bioinformatics/btz305.
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.
Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A

Bioinformatics. 2014 May 1;30(9):1312-3. doi: 10.1093/bioinformatics/btu033. Epub 2014 Jan 21.
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Stamatakis A.

S.A. Berger, D. Krompaß, A. Stamatakis:
“Performance, Accuracy and Web-Server for Evolutionary Placement of Short Sequence Reads under maximum-likelihood“.
Systematic Biology 60(3):291-302, 2011.

DIYABC 2.1.0 – Approximate Bayesian Computation for Inference on Population history

DIYABC 2.1.0

:: DESCRIPTION

DIYABC is a computer program with a graphical user interface and a fully click-able environment. It allows population biologists to make inference based on Approximate Bayesian Computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIYABC can be used to compare competing scenarios, estimate parameters for one or more scenarios, and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data).

::DEVELOPER

The Center for Biology and Management of Populations @ CBGP

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 DIYABC

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 13.
DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data.
Cornuet JM1, Pudlo P, Veyssier J, Dehne-Garcia A, Gautier M, Leblois R, Marin JM, Estoup A.

BMC Bioinformatics. 2010 Jul 28;11:401.
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0).
Cornuet JM, Ravigné V, Estoup A.

GIFT 1.0.0 – Global Optimization-based Inference of Chemogenomic Features from Drug-Target Interactions

GIFT1.0.0

:: DESCRIPTION

GIFT is a C++ package to infer the chemogenomic features from drug-target interactions.

::DEVELOPER

GIFT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • C++ Compiler

:: DOWNLOAD

 GIFT

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Mar 29. pii: btv181.
Global Optimization-based Inference of Chemogenomic Features from Drug-Target Interactions.
Zu S, Chen T, Li S

MaRIboES 2.1.0 – Metabolite and Reaction Inference based on Enzyme Specificities

MaRIboES 2.1.0

:: DESCRIPTION

MaRIboES is an algorithm for metabolite and reaction inference based on enzyme specificities. MaRIboES ,has many applications, for example to complete reconstructed metabolic networks, to aid in metabolic engineering or to help identify unknown peaks in mass spectra. MaRIboES employs structural and stereochemistry similarity measures and molecular fingerprints to generalise enzymatic reactions based on data available in BRENDA.

::DEVELOPER

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Matlab
  • C++ Compiler

:: DOWNLOAD

  MaRIboES

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Nov 15;25(22):2975-82. Epub 2009 Aug 20.
Metabolite and reaction inference based on enzyme specificities.
de Groot MJ, van Berlo RJ, van Winden WA, Verheijen PJ, Reinders MJ, de Ridder D.

PAINT 2.24 – Phylogenetic Annotation and INference Tool

PAINT 2.24

:: DESCRIPTION

PAINT is a java application for viewing tree files. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.

::DEVELOPER

Paul D. Thomas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

 PAINT

:: MORE INFORMATION

Citation

Brief Bioinform. 2011 Sep;12(5):449-62. Epub 2011 Aug 27.
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.
Gaudet P, Livstone MS, Lewis SE, Thomas PD.

GapAdj – Ancestral Genome Inference program

GapAdj

:: DESCRIPTION

GapAdj (Gapped-Adjacencies) is a generalization of DirectAdj accounting for α-adjacencies for increasing values of α

::DEVELOPER

NADIA EL-MABROUK

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GapAdj

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 19:S4. doi: 10.1186/1471-2105-13-S19-S4. Epub 2012 Dec 19.
A flexible ancestral genome reconstruction method based on gapped adjacencies.
Gagnon Y, Blanchette M, El-Mabrouk N.

Ortheus 0.5 – Inference of Ancestor (aka tree) Alignments

Ortheus 0.5

:: DESCRIPTION

Ortheus is a probabilistic method for the inference of ancestor (aka tree) alignments.It is primarily aimed at refining an initial (large-scale) genomic multiple-sequence alignment to create a multiple sequence ancestor alignment.

::DEVELOPER

Benedict Paten (benedict (AT) soe.ucsc.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Python
  • C Compiler

:: DOWNLOAD

   Ortheus

:: MORE INFORMATION

Citation

Genome Res. 2008 Nov;18(11):1814-28. doi: 10.1101/gr.076554.108. Epub 2008 Oct 10.
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
Paten B, Herrero J, Beal K, Fitzgerald S, Birney E.

Optimist 20130226 – Inference of Positive Selection

Optimist 20130226

:: DESCRIPTION

Optimist is a simple software package for inferring positive selection from marker dynamics in an asexual population.

::DEVELOPER

Chris Illingworth.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 Optimist

:: MORE INFORMATION

Citation

A method to infer positive selection from marker dynamics in an asexual population.
Illingworth CJ and Mustonen V
Bioinformatics (Oxford, England) 2012;28;6;831-7

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