Concaterpillar is a hierarchical likelihood-ratio test for phylogenetic congruence.
Remarque If you use Concaterpillar for a publication please cite: Leigh JW, Susko E, Baumgartner M, Roger AJ. Testing congruence in phylogenomic analysis. Syst Biol. 2008 Feb; 57(1): 104-15.
|Run Unix # concaterpillar.py||Run Web #|
CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection. CONSEL does not estimate the phylogenetic tree by itself, but CONSEL does read the output of the other phylogenetic packages, such as Molphy, PAML, PAUP*, TREE-PUZZLE, and PhyML. CONSEL calculates the p-value using several testing procedures; the bootstrap probability, the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and the weighted Shimodaira-Hasegawa test. In addition to these conventional tests, CONSEL calculates the p-value based on the approximately unbiased test using the multi-scale bootstrap technique. This newly developed method gives less biased results than the conventional methods.
|Run Unix #||Run Web #|
Parses microbial profiles and, because gene copy number (GCN) estimates are pre-computed for all taxa in the reference taxonomy, rapidly corrects GCN bias. The CopyRighter bioinformatic tools permits rapid correction of GCN in microbial surveys, resulting in improved estimates of microbial abundance, alpha and beta diversity.
|Run Unix # copyrighter -i [optional arguments]||Run Web #|
indel-Seq-Gen (iSG) is a biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies. This is accomplished through the addition of subsequence length constraints and lineage- and site-specific evolution. iSG tracks insertion and deletion processes that occur during the simulation run. iSG records all evolutionary events and outputs the "true" multiple alignment of the sequences, and can generate a larger simulated sequence space by allowing the use of multiple related root sequences. iSG can be used to test the accuracy of multiple alignment methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein superfamily classification methods. iSG utilizes a highly modified version of the substitution engine from Seq-Gen v1.3.2.
|Run Unix # indel-seq-gen [-bdefghilmnoqsuwz] < [tree_file] (indel-seq-gen -h)||Run Web #|
ModelGenerator is a model selection program that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models.
|Run Unix # modelgenerator||Run Web #|
Modeltest est un programme qui évalue différents tests de rapport de vraisemblance de modèles d'évolution dans le but de choisir le modèle le plus approprié aux données.
|Run Unix # modeltest||Run Web #|
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
|Run Unix # mb||Run Web #|
NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
|Run Unix # njplot||Run Web #|
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.
|Run Unix # #baseml (basemlg codeml pamp evolver yn00 chi2)||Run Web #|
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 (see left panel). For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.
|Run Unix # phast||Run Web #|
PHYLIP is a free package of programs for inferring phylogenies.
|Run Unix # dnaml||Run Web # http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html|
PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction and molecular dating using protein and nucleic acid alignments. Compared to other phylogenetic MCMC samplers, the main distinguishing feature of PhyloBayes is the use of nonparametric methods for modelling site-specific features of sequence evolution.
|Run Unix #||Run Web #|
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. Since the original publication (Guindon and Gascuel 2003), PhyML has been widely used (>1,250 citations in ISI Web of Science), due to its simplicity and a fair accuracy/speed compromise. In the mean time research around PhyML has continued. We designed an efficient algorithm to search the tree space using Subtree Pruning and Regrafting (SPR) topological moves (Hordijk and Gascuel 2005), and proposed a fast branch test based on an approximate likelihood ratio test (Anisimova and Gascuel 2006). However, these novelties were not included in the official version of PhyML, and we found that improvements were still needed in order to make them effective in some practical cases. PhyML 3.0 achieves this task. It implements new algorithms to search the space of tree topologies with user-defined intensity. A non-parametric, Shimodaira-Hasegawa-like branch test is also available. The program provides a number of new evolutionary models and its interface was entirely re-designed. We tested PhyML 3.0 on a large collection of real data sets to ensure that the new version is stable, ready-to-use and still reasonably fast and accurate.
|Run Unix # phyml||Run Web #|
PROTTEST3 is a high-performance computing program for selecting the model of protein evolution that best fits a given set of aligned sequences. This java program uses the Phyml program (for maximum likelihood calculations and optimization of parameters) and the PAL library for handling trees, and the ALTER library for reading aligment formats. Empirical models included are as WAG, LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam, MtArt, HIVb/HIVw and FLU, plus +I:invariable sites, +G: rate heterogeneity among sites and +F: observed amino acid frequencies. ProtTest uses the Akaike Information Criterion (AIC) and other statistics (AICc, BIC and DT) to find which of the candidate models best fits the data at hand. It also implements the calculation of model-averged phylogenies.
Remarque Citation: Darriba D, Taboada GL, Doallo R, Posada D. In press. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics.
|Run Unix # runProtTestHPC ou runXProtTestHPC||Run Web #|
QuickTree is a program for the rapid reconstruction of phylogenies by the Neighbor-Joining method. For details, see the article published in the journal 'Bioinformatics' (18:1546-1547).
|Run Unix # quicktree||Run Web #|
RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood  based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP  package.
Remarque If you use RAxML please always cite the following paper: Alexandros Stamatakis : “RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models”, Bioinformatics 22(21):2688–2690, 2006 .
|Run Unix # raxmlHPC -h ou raxmlHPC-MPI -h||Run Web #|
Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.
|Run Unix # seq-gen||Run Web #|
SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.
|Run Unix # SplitsTree||Run Web #|
TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREEPUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated with and without the molecular-clock assumption. In addition, TREE-PUZZLE o ers likelihood mapping, a method to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio to test the clock hypothesis, one and two-sided Kishino-Hasegawa test, Shimodaira-Hasegawa test, Expected Likelihood Weights). The models of substitution provided by TREE-PUZZLE are GTR, TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters (except for GTR) can be inferred from the data set.
|Run Unix # puzzle||Run Web #|