Genie 3.0 – Estimating Demographic History from Molecular Phylogenies

Genie 3.0

:: DESCRIPTION

Genie (Genealogy Interval Explorer) is a program for the inference of demographic history from reconstructed molecular phylogenies. It is primarily designed for the analysis of phylogenies reconstructed from highly variable viral gene sequences, but can be applied to other types of sequence data that contains a significant amount of phylogenetic information.

::DEVELOPER

Genie team

:: REQUIREMENTS

  • Windows /  MacOSX

:: DOWNLOAD

 Genie

:: MORE INFORMATION

Citation:

Pybus OG, Rambaut. A. 2002.
GENIE: Estimating demographic history from molecular phylogenies.
Bioinformatics 18:1404-5

PASSML / Passml_TM – Analysis of Phylogeny / Transmembrane Domain searching from Aligned Amino Acid Sequences

PASSML / Passml_TM

:: DESCRIPTION

PASSML (‘Phylogeny and Secondary Structure using Maximum Likelihood’) has been developed to implement an evolutionary model that combines protein secondary structure and amino acid replacement.

Passml_TM implement an evolutionary model that permits analysis of phylogeny and transmembrane domain searching from aligned amino acid sequences.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PASSML / Passml_TM

:: MORE INFORMATION

Citation

Bioinformatics. 1998;14(8):726-33.
PASSML: combining evolutionary inference and protein secondary structure prediction.
Liò P, Goldman N, Thorne JL, Jones3 DT.

EDIBLE 20110705 – Make Phylogenetic Information Calculations

EDIBLE 20110705

:: DESCRIPTION

EDIBLE (Experimental Design and Information By Likelihood Exploration.) is a software to perform likelihood calculations based on Markov process models of nucleotide substitution allied with phylogenetic trees, and from these to compute Fisher information measures under different experimental designs. These calculations can be used to answer questions of optimal experimental design in molecular phylogenetics.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 EDIBLE

:: MORE INFORMATION

Citation:

EDIBLE: experimental design and information calculations in phylogenetics.
Massingham T, Goldman N.
Bioinformatics. 2000 Mar;16(3):294-5.

RATS 1.0 – Resource Aware Taxon Selection

RATS 1.0

:: DESCRIPTION

RATS (Resource Aware Taxon Selection)

The phylogenetic diversity (PD) of a set of taxonomical units (e.g. genes, individuals, populations, species) is the total length of the evolutionary tree connecting them. This measure is relevant for choosing taxa in a variety of applications. In comparative genomics, the statistical power in testing various evolutionary hypotheses (e.g. low substitution rates) and in finding interesting genomic features (e.g. protein-coding genes, noncoding conserved elements) is strongly correlated with the total PD of the sequences being compared. Therefore, sequencing projects (both at the genome and gene level) should target taxa with a high total PD (see [1] and references therein). In biodiversity conservation, when not all species or populations in a geographical area can be protected, it is reasonable to concentrate conservation efforts on a subset with maximum PD [2].

Given the growing interest in PD, Fabio Pardi has worked on a hierarchy of optimisation problems where the aim is to select, from a collection of candidate taxa, a subset with maximum total PD. Depending on the nature of the constraints on this subset, the problems have varying computational complexity and different algorithmic solutions are devisable. When the aim is to select a fixed number of taxa, a simple greedy algorithm can be shown to produce optimal solutions [1]. When different taxa require different amounts of resources (money, time, etc.) for their selection (sequencing or conservation) and we have a limit on the total amount of resources available, however, it transpires that the problem is more difficult. We have devised a novel dynamic programming algorithm that can compute the optimal solution efficiently [3].

This algorithm is implemented by the program rats.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX

:: DOWNLOAD

 RATS

:: MORE INFORMATION

Citation:

Syst Biol. 2007 Jun;56(3):431-44.
Resource-aware taxon selection for maximizing phylogenetic diversity.
Pardi F, Goldman N.

PhyloSim 3.0.5 – Monte Carlo Simulation of Sequence Evolution

PhyloSim 3.0.5

:: DESCRIPTION

PhyloSim is an extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhyloSim

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Apr 19;12:104.
PhyloSim – Monte Carlo simulation of sequence evolution in the R statistical computing environment.
Sipos B, Massingham T, Jordan GE, Goldman N.

DIVEIN – Analyze Phylogenies, Sequence Divergence, Diversity and Informative Sites

DIVEIN

:: DESCRIPTION

DIVEIN is a web service that performs automated maximum likelihood phylogenetic analyses of nucleotide and amino acid sequences. Starting with a set of aligned sequences

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Biotechniques. 2010 May;48(5):405-8. doi: 10.2144/000113370.
DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites.
Deng W1, Maust BS, Nickle DC, Learn GH, Liu Y, Heath L, Kosakovsky Pond SL, Mullins JI.

DiverAnalysis – Analysis of Sequence Divergence and Diversity

DiverAnalysis

:: DESCRIPTION

DiverAnalysis is designed to perform phylogenetic analyses of sequence divergence and diversity.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 DiverAnalysis

:: MORE INFORMATION

SPECTRE 1.1.5 – Suite of Phylogenetic tools for Reticulate Evolution

SPECTRE 1.1.5

:: DESCRIPTION

SPECTRE provides several new implementations of pre-published algorithms to construct phylogenetic trees and networks (more precisely split networks), along with an interactive graphical interface for visualizing planar split networks.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SPECTRE 

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Mar 15;34(6):1056-1057. doi: 10.1093/bioinformatics/btx740.
SPECTRE: a suite of phylogenetic tools for reticulate evolution.
Bastkowski S, Mapleson D, Spillner A, Wu T, Balvociute M, Moulton V.

MetaPIGA v3.1 – Large Phylogeny Estimation

MetaPIGA v3.1

:: DESCRIPTION

MetaPIGA is a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a random-restart hill climbing, a simulated annealing algorithm, a classical genetic algorithm, and the metapopulation genetic algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data.

::DEVELOPER

Laboratory of Artificial & Natural Evolution

:: SCREENSHOTS

MetaPIGA

:: REQUIREMENTS

  • MacOsX / Linux / Windows
  • Java

:: DOWNLOAD

  MetaPIGA

:: MORE INFORMATION

Citation

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics
aphaël Helaers & Michel C. Milinkovitch
BMC Bioinformatics 2010, 11:379

Gblocks 0.91b – Selection of Conserved Blocks from multiple alignments for their use in Phylogenetic Snalysis

Gblocks 0.91b

:: DESCRIPTION

Gblocks is a computer program written in C that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis.

::DEVELOPER

Castresana Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX

:: DOWNLOAD

  Gblocks

:: MORE INFORMATION

Citation:

Talavera, G., and Castresana, J. (2007).
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
Systematic Biology 56, 564-577.