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.
Chen, W.-C
verlapping Codon model, Phylogenetic Cluetering, and Alternative Partial Expectation Conditional Maximization Algorithm
Ph.D. Diss., Iowa Stat University (2011)
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.
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.
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.
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.
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.
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.
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.
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.