ProtEvol 1.0 – Maximum Likelihood Phylogenetic Inference with Selection on Protein Folding Stability

ProtEvol 1.0

:: DESCRIPTION

The program ProtEvol performs two kinds of computation.

  1. It computes the mean-field site-specific amino acid distributions that have minimal differences with respect to the background distribution and that constraint the average stability of the native state of the protein against both unfolding and misfolding. The program also computes an exchangeability matrix derived from an empirical substitution model or from a mutation model that can be used together with the site-specific distributions for applications in phylogenetic inference.
  2. It simulates protein evolution subject to the constraint of selection on the folding stability of the native state of the protein against both unfolding and misfolding.

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  ProtEvol

:: MORE INFORMATION

Citation

Maximum likelihood phylogenetic inference with selection on protein folding stability.
Arenas M, Sánchez-Cobos A, Bastolla U.
Mol Biol Evol. 2015 Apr 2. pii: msv085.

LAMARC 2.1.10 – Maximum Likelihood & Bayesian Estimation of Population Parameters

LAMARC 2.1.10

:: DESCRIPTION

LAMARC (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates. It approximates a summation over all possible genealogies that could explain the observed sample, which may be sequence, SNP, microsatellite, or electrophoretic data.

::DEVELOPER

Felsenstein/Kuhner lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

LAMARC

:: MORE INFORMATION

Citation:

Mary K. Kuhner
LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
Bioinformatics (2006) 22 (6): 768-770.

deML v1.1.3 – Maximum Likelihood Demultiplexing for NGS data

deML v1.1.3

:: DESCRIPTION

deML is a program for maximum likelihood demultiplexing of next-generation sequencing data.

::DEVELOPER

Department of Genetics / Bioinformatics Group, Max Planck Institute for Evolutionary Anthropology, Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 deML

:: MORE INFORMATION

Citation

deML: Robust demultiplexing of Illumina sequences using a likelihood-based approach.
Renaud G, Stenzel U, Maricic T, Wiebe V, Kelso J.
Bioinformatics. 2014 Oct 30. pii: btu719.

Partition 2.0 / PartitionML / PartitionView – maximum likelihood / Identifying Population Sub-division & Assigning Individuals to Populations

Partition 2.0 / PartitionML / PartitionView

:: DESCRIPTION

Partition is a model-based statistical software package for identifying population sub-division and assigning individuals to populations, on the basis of their genotypes at co-dominant marker loci. The underlying population genetic model is appropriate for out-crossing diploid organisms.

PartitionML is a program that searches for the best possible partition of a sample into independent panmictic clusters and simultaneously assign individuals to them using a maximum likelihood (ML) criterion.

PartitionView will read the  partition output file, as it is being written, and will display the path of the Markov chain (see below) as it evolves in real time.

::DEVELOPER

Partition team

:: SCREENSHOTS

Partition

PartitionView

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Partition  / PartitionML

:: MORE INFORMATION

Citation

Heredity (Edinb). 2009 Jul;103(1):32-45. doi: 10.1038/hdy.2009.29. Epub 2009 Apr 1.
An agglomerative hierarchical approach to visualization in Bayesian clustering problems.
Dawson KJ1, Belkhir K.

Heredity (Edinb). 2002 Jul;89(1):27-35.
Heterozygote deficiencies in small lacustrine populations of brook charr Salvelinus Fontinalis Mitchill (Pisces, Salmonidae): a test of alternative hypotheses.
Castric V1, Bernatchez L, Belkhir K, Bonhomme F.

MLGO – Maximum Likelihood for Gene Order Analysis

MLGO

:: DESCRIPTION

MLGO is a web server designed for genome rearrangement and gene order analysis. It can be used to infer a phylogeny from genome rearrangement and gene order data, and can also obtain an estimation of ancestral genomes, given an input tree. It can handle large scale data with the size ranges from mitochandrial to nuclear genomes. Besides rearrangements, it can also handle gene insertion, deletion and duplication.

::DEVELOPER

Jijun Tang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Nov 8;15(1):354. [Epub ahead of print]
MLGO: phylogeny reconstruction and ancestral inference from gene-order data.
Hu F, Lin Y, Tang J.

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.

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.

PhyML 2020 – Phylogeny software based on the Maximum Likelihood

PhyML 2020

:: 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.

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.

stochprofML 2.0.3 – Stochastic Profiling using Maximum Likelihood Estimation

stochprofML 2.0.3

:: 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:

Amrhein L, Fuchs C.
stochprofML: stochastic profiling using maximum likelihood estimation in R.
BMC Bioinformatics. 2021 Mar 15;22(1):123. doi: 10.1186/s12859-021-03970-7. PMID: 33722188; PMCID: PMC7958472.