:: DESCRIPTION
SNPPar is designed to find homoplasic SNPs based on a user-defined phylogenetic tree
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Edwards DJ, Duchene S, Pope B, Holt KE.
SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.
Microb Genom. 2021 Dec;7(12). doi: 10.1099/mgen.0.000694. PMID: 34874243.
:: DESCRIPTION
phyclust (Phyloclustering) is a software package for evolutionary clustering of sequence data.An evolutionary Continuous Time Markov Chain model-based approach is developed to determine population structure from molecular data without assuming linkage equilibrium. The phyclust is designed in C for performance and interfaced with R for visualization, and sets up a common platform and incorporates other popular open source software for simulating data and additional analyses.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chen, W.-C
verlapping Codon model, Phylogenetic Cluetering, and Alternative Partial Expectation Conditional Maximization Algorithm
Ph.D. Diss., Iowa Stat University (2011)
:: DESCRIPTION
ScripTree would enable the saving of graphical analyses involving numerous and complex tree handling operations and would allow the automation of repetitive tasks.ScripTree is a tool intended to fill this gap. It is an interpreter to be used in batch mode. Phylogenetic graphics instructions are stored in a text file and performed in a sequential way. Such instructions are related to tree rendering as well as tree annotation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Apr 15;26(8):1125-6. Epub 2010 Mar 1.
ScripTree: scripting phylogenetic graphics.
Chevenet F, Croce O, Hebrard M, Christen R, Berry V.
:: DESCRIPTION
phylolm is an R package providing a function for fitting phylogenetic linear regression models. The likelihood is calculated with an algorithm that is linear in the number of tips in the tree. The package also provides a function for simulating continuous traits along the tree.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Syst Biol. 2014 Feb 4. [Epub ahead of print]
A linear-time algorithm for Gaussian and non-Gaussian trait evolution models.
Ho LS, Ané C.
:: DESCRIPTION
MEGA （Molecular Evolutionary Genetics Analysis）is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Biol Evol. 2013 Dec;30(12):2725-9. doi: 10.1093/molbev/mst197. Epub 2013 Oct 16.
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011)
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods.
Molecular Biology and Evolution (2011)doi: 10.1093/molbev/msr121 First published online: May 4, 2011
:: DESCRIPTION
SEMPHY is a tool for data-intensive phylogenetic reconstruction. SEMPHY infers phylogenies by Maximum Likelihood, the most established criterion for finding the correct phylogenetic tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2007 Jan 15;23(2):e136-41.
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates.
Ninio M, Privman E, Pupko T, Friedman N.
:: DESCRIPTION
RAP is an algorithm and a software have been developed, which permit to find gene duplications in phylogenetic trees, in order to improve gene function inferences. The algorithm is applicable to realistic data, especially n-ary species tree and unrooted phylogenetic tree
RAP-Green is a new implementation and an improvment of the RAP software which permits to compare gene and species trees, infers duplication events, and provide confidence score in function conservation between genes.
::DEVELOPER
South Green bioinformatics platform
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Dufayard JF, Bocs S, Guignon V, Larivière D, Louis A, Oubda N, Rouard M, Ruiz M, de Lamotte F.
RapGreen, an interactive software and web package to explore and analyze phylogenetic trees.
NAR Genom Bioinform. 2021 Sep 23;3(3):lqab088. doi: 10.1093/nargab/lqab088. PMID: 34568824; PMCID: PMC8459725.
:: DESCRIPTION
PrIME (Probabilistic Integrated Models of Evolution) is a library and accompanying tools for phylogenetics. PrIME mainly relies on Markov-chain Monte Carlo (MCMC) framework and probabilistic modeling.
::DEVELOPER
the Science for Life Laboratory, Uppsala University,
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Integrating Sequence Evolution into Probabilistic Orthology Analysis.
Ullah I, Sjöstrand J, Andersson P, Sennblad B, Lagergren J.
Syst Biol. 2015 Nov;64(6):969-82. doi: 10.1093/sysbio/syv044
:: DESCRIPTION
Saguaro (Genome-Wide) , SaguaroGW,is a program to detect signatures of selection within populations, strains, or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in the genome.
::DEVELOPER
the Science for Life Laboratory, Uppsala University, and the Broad Institute of MIT and Harvard.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Genomics. 2013 May 24;14:347. doi: 10.1186/1471-2164-14-347.
Unsupervised genome-wide recognition of local relationship patterns.
Zamani N1, Russell P, Lantz H, Hoeppner MP, Meadows JR, Vijay N, Mauceli E, di Palma F, Lindblad-Toh K, Jern P, Grabherr MG.
:: DESCRIPTION
MaxTiC (Maximum Time Consistency) is a software which takes as input a species tree and a series of (possibly inconsistent) time constraints between its internal nodes, weighted by confidence scores.
::DEVELOPER
Computational Methods for Paleogenomics and Comparative Genomics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
