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.

Phylonium 1.4 – Fast and Accurate Estimation of Evolutionary Distances

Phylonium 1.4

:: DESCRIPTION

Phylonium is a program for estimating the evolutionary distances between closely related genomes. It is much faster than alignment based approaches for phylogeny reconstruction and usually more accurate than competing alignment-free methods.

::DEVELOPER

Fabian Klötzl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Phylonium

:: MORE INFORMATION

Citation

Klötzl F, Haubold B.
Phylonium: fast estimation of evolutionary distances from large samples of similar genomes.
Bioinformatics. 2020 Apr 1;36(7):2040-2046. doi: 10.1093/bioinformatics/btz903. PMID: 31790149; PMCID: PMC7141870.

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

MixTreEM – Species Tree Inference Using a Mixture Model

MixTreEM

:: DESCRIPTION

MixTreEM (Mixture of Trees using Expectation Maximization) is a species tree reconstruction method.

::DEVELOPER

MixTreEM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MixTreEM

:: MORE INFORMATION

Citation:

Species Tree Inference Using a Mixture Model.
Ullah I, Parviainen P, Lagergren J.
Mol Biol Evol. 2015 Sep;32(9):2469-82. doi: 10.1093/molbev/msv115.

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

PrIME  team

:: 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

POPTREE 2 / POPTREEW – Make Population Trees from Allele Frequency data

POPTREE 2 / POPTREEW

:: DESCRIPTION

POPTREE is a program for making population trees from allele frequency data

POPTREEW is a web version of POPTREE for construction of population trees from allele frequency data and computing other quantities

::DEVELOPER

Naoko Takezaki

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Unix

:: DOWNLOAD

 PopTree

:: MORE INFORMATION

Citation:

POPTREEW: web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities.
Takezaki N, Nei M, Tamura K.
Mol Biol Evol. 2014 Jun;31(6):1622-4. doi: 10.1093/molbev/msu093

POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface.
Takezaki N, Nei M, Tamura K.
Mol Biol Evol. 2010 Apr;27(4):747-52. Epub 2009 Dec 18.

Bosque 2.0.2 – Phylogenetic Analysis Software

Bosque 2.0.2

:: DESCRIPTION

Bosque is a distributed software environment oriented to manage the computational resources involved in typical phylogenetic analyses. Bosque has been implemented as a client-server application where the server  can execute installed phylogenetic programs (Phylip, PhyML, TreePuzzle, Muscle) and the client manages the results on a local relational database, although it can also execute phylogenetic programs locally, useful when no server is available. The client also performs the graphical visualisation and edition of trees and alignments, providing an environment for the analyses, from the integration of sequences to the printing of a final tree.

::DEVELOPER

Millenium Institute of Oceanography

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Bosque

:: MORE INFORMATION

Citation:

Ramírez-Flandes S. & O. Ulloa(2008).
Bosque: Integrated phylogenetic analysis software.
Bioinformatics 24(21):2539-2541; doi: 10.1093/bioinformatics/btn466

QueTAL 1.1 – A suite for the Functional and Phylogenetic Comparison of TAL effectors

QueTAL 1.1

:: DESCRIPTION

QueTAL is a suite of tools to classify and compare TAL (Transcription Activator-Like) effectors functionally and phylogenetically.

::DEVELOPER

QueTAL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  QueTAL

:: MORE INFORMATION

Citation

QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically.
Pérez-Quintero AL, Lamy L, Gordon JL, Escalon A, Cunnac S, Szurek B, Gagnevin L.
Front Plant Sci. 2015 Aug 3;6:545. doi: 10.3389/fpls.2015.00545.

bdvis 0.2.28 – Biodiversity Data Visualizations

bdvis 0.2.28

:: DESCRIPTION

bdvis provides a set of functions to create basic visualizations to quickly preview different aspects of biodiversity information such as inventory completeness, extent of coverage (taxonomic, temporal and geographic), gaps and biases.

::DEVELOPER

Vijay Barve

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R

:: DOWNLOAD

 bdvis

:: MORE INFORMATION

Citation

bdvis: visualizing biodiversity data in R.
Barve V, Otegui J.
Bioinformatics. 2016 Jun 10. pii: btw333.

MetaTreeMap 3.2 – An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees

MetaTreeMap 3.2

:: DESCRIPTION

MetaTreeMap (MTM) is a module developed to visualize phylogenic trees where each species (node) has a number of reads (quantity) that map on the reference genome of this species. Each species is represented by a rectangle and its area is proportional to the number of assigned reads. The final figure is nested rectangles representing tree branches.

::DEVELOPER

Maxime HEBRARD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Javascript

:: DOWNLOAD

 MetaTreeMap

:: MORE INFORMATION

Citation

PLoS One. 2016 Jun 23;11(6):e0158261. doi: 10.1371/journal.pone.0158261. eCollection 2016.
MetaTreeMap: An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees.
Hebrard M, Taylor TD.