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.

Phy2HTML 1.0 – Display Phylogeny using only HTML and CSS

Phy2HTML 1.0

:: DESCRIPTION

Phy2HTML is a simple Python program that is designed to read a tree in Newick format and create a visualization of the tree for display in a webpage using only HTML and CSS.

::DEVELOPER

Michael S. Rosenberg’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

Phy2HTML

:: MORE INFORMATION

Seq-Gen 1.3.4 – Simulate the Evolution of Sequences along a Phylogeny

Seq-Gen 1.3.4

:: DESCRIPTION

Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Seq-Gen

:: MORE INFORMATION

Citation

Comput Appl Biosci. 1997 Jun;13(3):235-8.
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.
Rambaut A1, Grassly NC.

CoevRJ – Jointly Estimate Phylogeny and Molecular Coevolution

CoevRJ

:: DESCRIPTION

CoevRJ is a new model and tool for the joint inference of coevolution and phylogeny.

::DEVELOPER

The Computational Phylogenetics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CoevRJ

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2019 Mar 12;116(11):5027-5036. doi: 10.1073/pnas.1813836116. Epub 2019 Feb 26.
Simultaneous Bayesian inference of phylogeny and molecular coevolution.
Meyer X, Dib L, Silvestro D, Salamin N

MrBayes 3.2.7a – Bayesian Inference of Phylogeny

MrBayes 3.2.7a

:: DESCRIPTION

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes’s theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

::DEVELOPER

MrBayes Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

MrBayes

:: MORE INFORMATION

Citation:

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP.
Syst Biol. 2012 May;61(3):539-42. doi: 10.1093/sysbio/sys029.

Ronquist F, Huelsenbeck JP.
MrBayes 3: Bayesian phylogenetic inference under mixed models.
Bioinformatics. 2003 Aug 12;19(12):1572-4.

RADIS 1.0.0 – Analysis of RAD-seq data for InterSpecific Phylogeny

RADIS 1.0.0

:: DESCRIPTION

RADIS is a perl pipeline which makes the processing of RAD-seq data easier and allows rapid and automated exploration of parameters/data for phylogenetic inference.

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 RADIS

:: MORE INFORMATION

Citation

RADIS: Analysis of RAD-seq data for InterSpecific phylogeny.
Cruaud A, Gautier M, Rossi JP, Rasplus JY, Gouzy J.
Bioinformatics. 2016 Jun 16. pii: btw352.

FastME 2.1.5 – Fast & Accurate Phylogeny Reconstruction

FastME 2.1.5

:: DESCRIPTION

FastME is a software for fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. FastME showed better topological accuracy than NJ, BIONJ, WEIGHBOR and FITCH, in all evolutionary conditions we tested, which include large range deviations from molecular clock and substitution rates. When the number of taxa is high, its superiority over NJ, BIONJ and WEIGHBOR becomes important, while FITCH remains close to FastME but becomes hard to use due to its slowness. FastME is very fast, even faster than NJ, and can easily be applied to very large data sets (> 1000 taxa).

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

FastME

:: MORE INFORMATION

Citation

Mol Biol Evol. 2015 Oct;32(10):2798-800. doi: 10.1093/molbev/msv150. Epub 2015 Jun 30.
FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program.
Lefort V, Desper R, Gascuel O

Desper R., Gascuel O.
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.
Journal of Computational Biology. 2002 9(5):687-705.

CompPhy – A Web-based Collaborative Platform for comparing Phylogenies

CompPhy

:: DESCRIPTION

CompPhy is a web platform dedicated to the collaborative handling of phylogenetic trees.

:: DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Evol Biol. 2014 Dec 14;14(1):253.
CompPhy: a web-based collaborative platform for comparing phylogenies.
Fiorini N, Lefort V, Chevenet F, Berry V, Chifolleau AM.

CellScape 0.99.3 – Visualization tool for integrating single Cell Phylogeny

CellScape 0.99.3

:: DESCRIPTION

CellScape is a visualization tool for integrating single cell phylogeny with genomic content to clearly display evolutionary progression and tumour heterogeneity.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

CellScape

:: MORE INFORMATION

CITUP v0.1.0 – Clonality Inference in Multiple Tumor Samples using Phylogeny

CITUP v0.1.0

:: DESCRIPTION

CITUP is a bioinformatics tool that can be used to infer tumor heterogeneity using multiple samples from a single patient. Given mutational frequencies for each sample, CITUP uses an optimization based algorithm to find the evolutionary tree best explaining the data.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • IBM ILOG CPLEX Optimization Studio

:: DOWNLOAD

 CITUP

:: MORE INFORMATION

Citation

Clonality Inference in Multiple Tumor Samples using Phylogeny.
Malikic S, McPherson AW, Donmez N, Sahinalp CS.
Bioinformatics. 2015 Jan 6. pii: btv003.