TNT 202106 – Phylogenetic Analysis under Parsimony

TNT 202106

:: DESCRIPTION

TNT (Tree Analysis using New Technology) is a program for phylogenetic analysis under parsimony , as well as extensive tree handling and diagnosis capabilities.

::DEVELOPER

TNT team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 TNT

:: MORE INFORMATION

Citation

Giribet G.
TNT: Tree Analysis Using New Technology.”.
Syst Biol. 2005;54:176-178.

DARwin 6.0.021 – Diversity and Phylogenetic Analysis

DARwin 6.0.021

:: DESCRIPTION

DARwin (Dissimilarity Analysis and Representation for Windows) is a software package developed for diversity and phylogenetic analysis on the basis of evolutionary dissimilarities.

::DEVELOPER

DARwin Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 DARwin

:: MORE INFORMATION

Citation:

Perrier, X., Flori, A. , Bonnot, F. (2003). Data analysis methods.
In: Hamon, P., Seguin, M., Perrier, X. ,Glaszmann, J. C. Ed., Genetic diversity of cultivated tropical plants. Enfield, Science Publishers. Montpellier. pp 43 – 76.

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

:: 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.

BEST 3.0 – Phylogenetic Analysis of Multilocus Data

BEST 3.0

:: DESCRIPTION

BEST (Bayesian Estimation of Species Trees)is a free phylogenetics program to estimate the joint posterior distribution of gene trees and species tree using multilocus molecular data that accounts for deep coalescence but not for other issues such as horizontal transfer or gene duplication.

::DEVELOPER

Phylogenetics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX/ Windows

:: DOWNLOAD

 BEST

:: MORE INFORMATION

Citation

BEST: Bayesian estimation of species trees under the coalescent model.
Liu L.
Bioinformatics. 2008 Nov 1;24(21):2542-3. doi: 10.1093/bioinformatics/btn484

PHAST 1.5 / RPHAST 1.6.9 – Phylogenetic Analysis with Space/Time Models / for R

PHAST 1.5 / RPHAST 1.6.9

:: DESCRIPTION

PHAST is a freely available software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations.

RPHAST: Phylogenetic Analysis with Space/Time Models… in R

::DEVELOPER

Siepel Lab, Pollard Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 PHAST / RPHAST 

 :: MORE INFORMATION

Citation

Brief Bioinform. 2011 Jan;12(1):41-51. doi: 10.1093/bib/bbq072. Epub 2010 Dec 21.
PHAST and RPHAST: phylogenetic analysis with space/time models.
Hubisz MJ1, Pollard KS, Siepel A.

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

diversitree 0.9-15 – Comparative Phylogenetic Analysis of Diversification in R

diversitree 0.9-15

:: DESCRIPTION

The “diversitree” package includes a number of comparative phylogenetic methods, mostly focussing on analysing diversification and character evolution.

::DEVELOPER

Rich FitzJohn

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • R package

:: DOWNLOAD

 diversitree

:: MORE INFORMATION

Citation

Richard G. FitzJohn
Diversitree: comparative phylogenetic analyses of diversification in R
Issue Methods in Ecology and Evolution Methods in Ecology and Evolution Volume 3, Issue 6, pages 1084–1092, December 2012

FISHtrees 3.2.0 – Phylogenetic Analysis of Multiprobe Fluorescence in situ Hybridization data

FISHtrees 3.2.0

:: DESCRIPTION

FISHtrees” is a software program:
1) to parse copy numbers of multiple Fluorescence In Situ Hybridization (FISH) probe signals in a single-cell assay;
2) to analyze probe signals across multiple single-cell assays in a patient data file;
3) to model tumorigenesis as a tree of tumor progression paths for a given probe on a given patient data file;
4) to merge multiple tumorigenesis trees to represent multiple probes on a given patient data file;
5) to compute consensus multiple joint tumorigenesis trees representing multiple patient data files into a network as a graph of tumor progression pathways.

::DEVELOPER

FISHtrees team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FISHtrees

:: MORE INFORMATION

Citation

Gertz EM, et al.
FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe.
PLoS One. 2016 Jun 30;11(6):e0158569. doi: 10.1371/journal.pone.0158569. PMID: 27362268; PMCID: PMC4928784.

Bioinformatics. 2013 Jul 1;29(13):i189-98. doi: 10.1093/bioinformatics/btt205.
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations.
Chowdhury SA1, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R.

Armadillo 1.1 – A simple pipeline system for Phylogenetic Analysis

Armadillo 1.1

:: DESCRIPTION

Armadillo is a workflow platform dedicated to phylogenetic as well as general bioinformatics analysis.

::DEVELOPER

Abdoulaye Banire Diallo

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/MacOsX
  • Java

:: DOWNLOAD

 Armadillo

:: MORE INFORMATION

Citation

PLoS One. 2012;7(1):e29903. doi: 10.1371/journal.pone.0029903. Epub 2012 Jan 11.
Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations.
Lord E1, Leclercq M, Boc A, Diallo AB, Makarenkov V.

phyloExpCM 0.32 – Phylogenetic Analysis with experimentally determined Codon Models

phyloExpCM 0.32

:: DESCRIPTION

phyloExpCM is a Python package to implement experimentally determined codom models of substitution for phylogenetics.

::DEVELOPER

Bloom Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 phyloExpCM

:: MORE INFORMATION

Citation

Bloom JD.
An experimentally determined evolutionary model dramatically improves phylogenetic fit.
Mol Biol Evol. 2014;31:1956-1978.