PrIME 1.0.5 – Library and Accompanying tools for Phylogenetics

PrIME 1.0.5

:: DESCRIPTION

PrIME (Probabilistic Integrated Models of Evolution) is a library and accompanying tools for phylogenetics. PrIME mainly relies on Markov-chain Monte Carlo (MCMC) framework and probabilistic modeling.

::DEVELOPER

Ikram Ullah

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PrIME

:: MORE INFORMATION

Citation:

Integrating Sequence Evolution into Probabilistic Orthology Analysis.
Ullah I, Sjöstrand J, Andersson P, Sennblad B, Lagergren J.
Syst Biol. 2015 Nov;64(6):969-82. doi: 10.1093/sysbio/syv044

πBUSS 1.3.8 – BEAST/BEAGLE utility for Sequence Simulation

πBUSS 1.3.8

:: DESCRIPTION

πBUSS is a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication, delegating computationally intensive tasks to the BEAGLE library and thus making full use of multi-core architectures.

::DEVELOPER

Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research

:: SCREENSHOTS

pibuss

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Java

:: DOWNLOAD

 πBUSS

:: MORE INFORMATION

Citation

Bielejec, F., Lemey, P., Carvalho, L. M., Baele, G., Rambaut, A., Suchard, M. A. (2014)
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.
BMC Bioinformatics 15:133.

BEAST 1.8.3 / BEAST2 2.4.1 – Bayesian Evolutionary Analysis of Molecular Sequences

BEAST 1.8.3 / BEAST2 2.4.1

:: DESCRIPTION

BEAST (Bayesian Evolutionary Analysis Samling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

BEAST 2 is an open source cross-platform program for Bayesian MCMC phylogenetic analysis of molecular sequences.

::DEVELOPER

The University of Auckland Computational Evolution Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

BEAST /BEAST2

:: MORE INFORMATION

Citation:

Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration.
Gavryushkina A, Welch D, Stadler T, Drummond AJ.
PLoS Comput Biol. 2014 Dec 4;10(12):e1003919. doi: 10.1371/journal.pcbi.1003919.

Alexei J Drummond and Andrew Rambaut
BEAST: Bayesian evolutionary analysis by sampling trees
BMC Evolutionary Biology 2007, 7:214doi:10.1186/1471-2148-7-214

ViralNet – Computing Network Structures in RNA Viral Populations

ViralNet

:: DESCRIPTION

ViralNet is an application for estimating reticulated structures of mixed viral populations.

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 ViralNet

:: MORE INFORMATION

Citation

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing
Donatien Fotso-Chedom, Pablo R. Murcia, Chris D. Greenman
arXiv:1407.7997

TriLoNet 1.0 – Construct Rooted Level-1 Phylogenetic Networks

TriLoNet 1.0

:: DESCRIPTION

TriLoNet is a Java software package created to construct rooted level-1 phylogenetic networks from aligned DNA sequence data. The software package consists of two modules:

TriLoNet – constructs level-1 phylogenetic networks from a dense collection of trinets
SeqTrinet – constructs a dense set of trinets from a multiple sequence alignment

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 TriLoNet

:: MORE INFORMATION

Citation

TriLoNet: Piecing Together Small Networks to Reconstruct Reticulate Evolutionary Histories.
Oldman J, Wu T, van Iersel L, Moulton V.
Mol Biol Evol. 2016 Apr 15. pii: msw068.

PIVO 2 – Phylogeny by IteratiVe Optimization

PIVO 2

:: DESCRIPTION

PIVO is a program that reconstructs ancestral gene orders on complex phylogenies. Because it uses the DCJ model, it can handle linear, circular, and multilinear genomes. PIVO is mainly targeted at reconstructing rerrangement histories of mitochondrial genomes.

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 PIVO

:: MORE INFORMATION

Citation

Albert Herencsár, Broňa Brejová .
An Improved Algorithm for Ancestral Gene Order Reconstruction.
In V. Kurkova, L. Bajer, V. Svatek, ed., Information Technologies – Applications and Theory (ITAT), number 1003 in CEUR-WS, pp. 46-53, Jasna, Slovakia, 2014.

SATIVA 0.9 – Semi-Automatic Taxonomy Improvement and Validation Algorithm

SATIVA 0.9

:: DESCRIPTION

SATIVA is a pipeline that uses Evolutionary Placement Algorithm (EPA) to identify taxonomically mislabeled sequences and suggest corrections.

::DEVELOPER

Alexey Kozlov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 SATIVA

:: MORE INFORMATION

Citation

Phylogeny-aware identification and correction of taxonomically mislabeled sequences.
Kozlov AM, Zhang J, Yilmaz P, Glöckner FO, Stamatakis A.
Nucleic Acids Res. 2016 May 10. pii: gkw396

DupLoCut – Duplication Loss Phylogeny by Cutting Planes

DupLoCut

:: DESCRIPTION

DupLoCut computes ancestral gene orders, given a phylogenetic tree and gene orders assigned to the leaves of the tree. It attempts to find the most parsimony assignment of gene orders under the duplication-loss evolutionary model.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

  DupLoCut

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Sep;20(9):643-59. doi: 10.1089/cmb.2013.0057.
The duplication-loss small phylogeny problem: from cherries to trees.
Andreotti S1, Reinert K, Canzar S.

Kraken 0.10.5-beta – Kraken Taxonomic Sequence Classification System

Kraken 0.10.5-beta

:: DESCRIPTION

Kraken is a very fast system for taxonomic classification of short or long DNA sequences from a microbiome or metagenomic sample.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 Kraken

:: MORE INFORMATION

Citation

Genome Biol. 2014 Mar 3;15(3):R46. doi: 10.1186/gb-2014-15-3-r46.
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood DE, Salzberg SL.

PDA 1.0.3 – Phylogenetic Diversity Analyzer

PDA 1.0.3

:: DESCRIPTION

PDA (Phylogenetic Diversity Algorithm)  is a software tool to analyze various aspects of PD and PD-related measures based on both phylogenetic trees and networks

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 PDA

:: MORE INFORMATION

Citation:

Split diversity in constrained conservation prioritization using integer linear programming.
Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger M, von Haeseler A.
Methods Ecol Evol. 2015 Jan;6(1):83-91.