RAxML 8.2.12 – Sequential and Parallel Maximum Likelihood based inference of large phylogenetic trees

RAxML 8.2.3

:: 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.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  RAxML

:: MORE INFORMATION

Citation

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.

tree-puzzle 5.3.rc16 – Maximum Likelihood Analysis

tree-puzzle 5.3.rc16

:: DESCRIPTION

TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREEPUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated with and without the molecular-clock assumption. In addition, TREE-PUZZLE o ers likelihood mapping, a method to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio to test the clock hypothesis, one and two-sided Kishino-Hasegawa test, Shimodaira-Hasegawa test, Expected Likelihood Weights). The models of substitution provided by TREE-PUZZLE are GTR, TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters (except for GTR) can be inferred from the data set.

::DEVELOPER

Heiko A. SchmidtArndt von Haeseler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

tree-puzzle

:: MORE INFORMATION

Citation

Schmidt, H.A., K. Strimmer, M. Vingron, and A. von Haeseler (2002)
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.
Bioinformatics. 18:502-504.

GAML 0.1 – Genome Assembly by Maximum Likelihood

GAML 0.1

:: DESCRIPTION

GAML is a prototype genome assembly tool based on maximizing likelihood of the assembly in a model encompaasing error rate, insert length and other features of indvidual sequencing technologies.

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GAML

:: MORE INFORMATION

Citation

GAML: genome assembly by maximum likelihood.
Boža V, Brejová B, Vinař T.
Algorithms Mol Biol. 2015 Jun 3;10:18. doi: 10.1186/s13015-015-0052-6.

FretTrace 1.0 – Maximum Likelihood Trajectories from Single-molecule FRET Experiments

FretTrace 1.0

:: DESCRIPTION

FretTrace is the implementation of a maximum likelihood based theory. Single molecule Fluorescence Resonance Energy Transfer (FRET) experiments are a powerful and versatile tool for studying conformational motions of single biomolecules at a millisecond time scale. Typically, the small number of recorded photons limits the achieved time resolution.

::DEVELOPER

Gunnar Schröder and Helmut Grubmüller

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux

:: DOWNLOAD

  FretTrace

:: MORE INFORMATION

Citation

G. F. Schroder and H. Grubmuller,
Maximum likelihood trajectories from single molecule fluorescence resonance energy transfer experiments
J. Chem. Phys. 119: 9920-9924 (2003)

ERATE 0.8 – Maximum Likelihood Phylogenetic Inference

ERATE 0.8

:: DESCRIPTION

erate is an extension of Joe Felsenstein’s DNAML program which treats insertions and deletions as evolutionary events, rather than ignoring them as missing data (which is what the most widely used phylogenetic inference programs all do).

::DEVELOPER

Elena Rivas, Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ERATE

:: MORE INFORMATION

Citation

Probabilistic Phylogenetic Inference with Insertions and Deletions.
E. Rivas, S. R. Eddy.
PLoS Comput. Biol., 4:e1000172, 2008.

stochprofML 1.2 – Stochastic Profiling using Maximum Likelihood Estimation

stochprofML 1.2

:: DESCRIPTION

stochprofML is an R package of parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles

::DEVELOPER

Biostatistics, Institute of Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
:: DOWNLOAD

 stochprofML

:: MORE INFORMATION

Citation:

Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):E626-35. doi: 10.1073/pnas.1311647111. Epub 2014 Jan 21.
Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles.
Bajikar SS1, Fuchs C, Roller A, Theis FJ, Janes KA.

PAML 4.8a / PAMLX 1.3.1 – Phylogenetic Analysis by Maximum Likelihood

PAML 4.8a / PAMLX 1.3.1

:: DESCRIPTION

PAML (Phylogenetic Analysis by Maximum Likelihood) is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (dN and dS) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use.

PAML-X: A GUI for PAML

::DEVELOPER

Ziheng Yang

:: SCREENSHOTS

PAMLX

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

PAML , PAML-X

:: MORE INFORMATION

Citation:

Yang, Z. 2007.
PAML 4: a program package for phylogenetic analysis by maximum likelihood.
Molecular Biology and Evolution 24: 1586-1591

Mol Biol Evol. 2013 Oct 24.
PAMLX: A Graphical User Interface for PAML.
Xu B, Yang Z.

PhyML 20141029 – Phylogeny software based on the Maximum Likelihood

PhyML 20141029

:: DESCRIPTION

PhyML (Phylogenetic estimation using Maximum Likelihood) is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology.

PhyML Online Version

::DEVELOPER

Stéphane GuindonOlivier Gascuel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

PhyML

:: MORE INFORMATION

Citation:

Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O.
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Systematic Biology, 59(3):307-21, 2010.

FastML 201401 – Server for computing Maximum Likelihood Ancestral Sequence Reconstruction

FastML 201401

:: DESCRIPTION

The FastML server is a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences.

:: DEVELOPER

Edmond J. Safra Center for Bioinformatics  at Tel-Aviv university.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FastML

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W580-4. doi: 10.1093/nar/gks498. Epub 2012 May 31.
FastML: a web server for probabilistic reconstruction of ancestral sequences.
Ashkenazy H1, Penn O, Doron-Faigenboim A, Cohen O, Cannarozzi G, Zomer O, Pupko T.

MTDFREML – Multiple-Trait Derivtive-Free Restricted Maximum Likelihood

MTDFREML

:: DESCRIPTION

MTDFREML is aset of programs for estimation of genetic (co)variances using multiple-trait derivative-free restricted maximum likelihood

::DEVELOPER

Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Fortron

:: DOWNLOAD

 MTDFREML

:: MORE INFORMATION

Citation

J Anim Sci. 1996 Nov;74(11):2586-97.
Multiple-trait Gibbs sampler for animal models: flexible programs for Bayesian and likelihood-based (co)variance component inference.
Van Tassell CP1, Van Vleck LD.