SSA 1.0 – Inference of Maximum Likelihood Phylogenetic Trees Using a Stochastic Search Algorithm

SSA 1.0

:: DESCRIPTION

SSA is a program for inferring maximum likelihood phylogenies from DNA sequences. Two versions of the program are available: one which assumes a molecular clock and one which does not make this assumption. The method for searching the space of trees for the ML tree is based on a simulated-annealing type algorithm and is described in the reference above. The program implements Felsenstein’s F84 model of nucleotide substitution and associated sub-models. The program estimates the ML tree and branch lengths, and can optionally estimate the transversion/transversion ratio. Upon termination, the program returns the k trees of highest likelihood found during the search, where k can be set by the user.

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 SSA

:: MORE INFORMATION

Citation

Salter, L. and D. Pearl. 2001.
Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees,
Systematic Biology 50(1): 7-17.

SSAMK – Inference of Maximum Likelihood Phylogenetic Trees for Morphological Data

SSAMK

:: DESCRIPTION

SSAMK uses a stochastic search algorithm for estimation of maximum likelihood phylogenetic trees for morphological data

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SSAMK

:: MORE INFORMATION

Citation

Syst Biol. 2001 Nov-Dec;50(6):913-25.
A likelihood approach to estimating phylogeny from discrete morphological character data.
Lewis PO.

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.

SCG 0.3.1 – Inference of Clonal Genotypes

SCG 0.3.1

:: DESCRIPTION

SCG(Single Cell Genotyper) is a software for inference of clonal genotypes using targeted single cell (nucleus) sequencing.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

SCG

:: MORE INFORMATION

Citation

Nat Methods. 2016 Jul;13(7):573-6. doi: 10.1038/nmeth.3867. Epub 2016 May 16.
Clonal genotype and population structure inference from single-cell tumor sequencing.
Roth A, McPherson A, Laks E, Biele J, Yap D, Wan A, Smith MA, Nielsen CB, McAlpine JN, Aparicio S, Bouchard-Côté A, Shah SP

CITUP v0.1.0 – Clonality Inference in Multiple Tumor Samples using Phylogeny

CITUP v0.1.0

:: DESCRIPTION

CITUP is a bioinformatics tool that can be used to infer tumor heterogeneity using multiple samples from a single patient. Given mutational frequencies for each sample, CITUP uses an optimization based algorithm to find the evolutionary tree best explaining the data.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • IBM ILOG CPLEX Optimization Studio

:: DOWNLOAD

 CITUP

:: MORE INFORMATION

Citation

Clonality Inference in Multiple Tumor Samples using Phylogeny.
Malikic S, McPherson AW, Donmez N, Sahinalp CS.
Bioinformatics. 2015 Jan 6. pii: btv003.

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.