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

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

PAMLX

:: 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.

TNT 201506 – Phylogenetic Analysis under Parsimony

TNT 201506

:: 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

Pablo Goloboff (pablogolo@csnat.unt.edu.ar), James Farris (msl-farr@nrm.se) , and Kevin Nixon

:: SCREENSHOTS

TNT

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 TNT

:: MORE INFORMATION

Citation

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

DARwin 6.0.010 – Diversity and Phylogenetic Analysis

DARwin 6.0.010

:: 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.

phangorn 1.99.14 – Phylogenetic Analysis in R

phangorn 1.99.14

:: DESCRIPTION

phangorn is a package for phylogenetic reconstruction and analysis in the R language.

::DEVELOPER

Klaus Peter Schliep (klaus.kschliep@snv.jussieu.fr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  phangorn

:: MORE INFORMATION

Citation

phangorn: phylogenetic analysis in R
Klaus Peter Schliep
Bioinformatics (2011) 27 (4): 592-593.

PHAST 1.3 / RPHAST 1.6 – Phylogenetic Analysis with Space/Time Models / for R

PHAST 1.3 / RPHAST 1.6

:: 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.

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.

Séance 0.11 – Reference-based Phylogenetic Analysis for 18S rRNA Studies

Séance 0.11

:: DESCRIPTION

Séance is a community analysis pipeline for the 18S rRNA marker gene incorporating homopolymer modelling for clustering 454 data, phylogenetic placement and visualisation.

::DEVELOPER

Löytynoja Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Séance

:: MORE INFORMATION

Citation:

Séance: reference-based phylogenetic analysis for 18S rRNA studies.
Medlar A, Aivelo T, Löytynoja A.
BMC Evol Biol. 2014 Nov 30;14(1):235. PMID: 25433763

MitoPhAST 1.0 – Mitogenome Phylogenetic Analysis of Sequences Tool

MitoPhAST 1.0

:: DESCRIPTION

MitoPhAST is a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes.

::DEVELOPER

MitoPhAST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • BIoPerl
  • Python
  • BioPython

:: DOWNLOAD

 MitoPhAST

:: MORE INFORMATION

Citation

MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes.
Tan MH, Gan HM, Schultz MB, Austin CM.
Mol Phylogenet Evol. 2015 Feb 23;85:180-188. doi: 10.1016/j.ympev.2015.02.009

Pebble 1.0 – Phylogenetic Analysis Application

Pebble 1.0

:: DESCRIPTION

Pebble (Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment) is a powerful application for Phylogenetic analysis. The primary purpose of Pebble is to provide tools for analysis and simulation of serially sampled sequence data (through maximum likelihood, and least-squares methods). Implemented forms of simulation include: trees, via a coalescent model, and sequence alignments, given an input tree and substitution model. Extra functionality includes data manipulation tools for sequence alignments and phylogenetic trees, as well as useful inbuilt alignment construction and editing facilities.

::DEVELOPER

the New Zealand Bioinformatics Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

 Pebble

:: MORE INFORMATION

Citation

Curr Protoc Bioinformatics. 2004 May;Chapter 6:Unit 6.8. doi: 10.1002/0471250953.bi0608s05.
Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences.
Goode M, Rodrigo AG.