:: DESCRIPTION
Physher is a maximum likelihood-based method for estimating evolutionary rates and divergence times from genetic data.
::DEVELOPER
SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: DOWNLOAD
:: MORE INFORMATION
Citation
Manuel Garber et al.
Identifying novel constrained elements by exploiting biased substitution patterns,
Bioinformatics 2009 25(12):i54-i62.
:: 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
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Varón, A., L. S. Vinh, W. C. Wheeler. 2010.
POY version 4: phylogenetic analysis using dynamic homologies.
Cladistics, 26:72-85.
:: 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
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: MORE INFORMATION
Citation
phangorn: phylogenetic analysis in R
Klaus Peter Schliep
Bioinformatics (2011) 27 (4): 592-593.
