physher v1.0.2 – Phylogenetic Analysis of Genetic data

physher v1.0.2

:: DESCRIPTION

Physher is a maximum likelihood-based method for estimating evolutionary rates and divergence times from genetic data.

::DEVELOPER

Mathieu Fourment

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Physher

:: MORE INFORMATION

Citation

Fourment M, Holmes EC.
Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data.
BMC Evol Biol. 2014 Jul 24;14:163. doi: 10.1186/s12862-014-0163-6. PMID: 25055743; PMCID: PMC4222489.

phyloMeta 1.3 – Phylogenetic Comparative Analyses with Meta-analysis

phyloMeta 1.3

:: DESCRIPTION

PhyloMeta is a program for integrating a phylogeny (in NEWICK format) into traditional meta-analysis. All the familiar statistics of meta-analysis are calculated (e.g., pooled effect sizes with 95%CI and homogeneity tests) and paired with the phylogenetically-independent equivalents to these statistics.

::DEVELOPER

The Lajeunesse Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 phyloMeta

:: MORE INFORMATION

Citation

phyloMeta: a program for phylogenetic comparative analyses with meta-analysis.
Lajeunesse MJ.
Bioinformatics. 2011 Sep 15;27(18):2603-4. doi: 10.1093/bioinformatics/btr438

Siphy 0.5 – SIte-specific PHYlogenetic analysis

Siphy 0.5

:: DESCRIPTION

Siphy (SIte-specific PHYlogenetic analysis) analyzes multiple sequence alignments and single outs bases or small regions that are undergoing selection by looking at reduction in substitution rates and unexpected detecting substitution patterns. A specific program to detect conserved transcription factor binding sites is also available.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX /Windows
  • Java

:: DOWNLOAD

  Siphy

:: MORE INFORMATION

Citation

Manuel Garber et al.
Identifying novel constrained elements by exploiting biased substitution patterns,
Bioinformatics 2009 25(12):i54-i62.

abioscripts – Facilitating Phylogenetic Analysis

abioscripts

:: DESCRIPTION

abioscrips is a Java program aimed at facilitating phylogenetic analysis, currently the main feature of the program is the Sequence Concat function that will take multiple files containing alignments of different regions and concatenate into one file in Nexus- and Fasta- format.

::DEVELOPER

Anders Larsson

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux /MacOsX
  • java

:: DOWNLOAD

 abioscrips

:: MORE INFORMATION

POY 5.1.1 – Phylogenetic Analysis of DNA and other data using Dynamic Homology

POY 5.1.1

:: DESCRIPTION

POY is a phylogenetic analysis program that supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc). POY is particular in that it can perform true alignment and phylogeny inference (i.e. input sequences need not to be prealigned). Insertions, deletions, and rearrangements, can then be included in the overall tree score (under Maximum Parsimony), or in the model (under Maximum Likelihood). A variety of heuristic algorithms have been developed for this purpose and are implemented in POY.

::DEVELOPER

Systematic Biology divisions of the AMNH

:: SCREENSHOTS

POY

:: REQUIREMENTS

  • MacOsX/ Windows / Linux

:: DOWNLOAD

 POY

:: MORE INFORMATION

Citation

Varón, A., L. S. Vinh, W. C. Wheeler. 2010.
POY version 4: phylogenetic analysis using dynamic homologies.
Cladistics, 26:72-85.

MulRF 1.2 – Phylogenetic Analysis using Multi-copy Gene Trees

MulRF 1.2

:: DESCRIPTION

MulRF is a platform-independent software program designed to infer species trees from incongruent multi-copy gene trees using a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science,Iowa State University

:: SCREENSHOTS

MulRF

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 MulRF

:: MORE INFORMATION

Citation

MulRF: a software package for phylogenetic analysis using multi-copy gene trees.
Chaudhary R, Fernández-Baca D, Burleigh JG.
Bioinformatics. 2014 Oct 1. pii: btu648.

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.

MitoPhAST 3.0 – Mitogenome Phylogenetic Analysis of Sequences Tool

MitoPhAST 3.0

:: 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

Séance 0.12 – Reference-based Phylogenetic Analysis for 18S rRNA Studies

Séance 0.12

:: 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

phangorn 2.7.1 – Phylogenetic Analysis in R

phangorn 2.7.1

:: 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.