Phylogenetics :: Inference

  • IQ-TREE (Efficient reconstruction of large maximum-likelihood phylogenies)
    An efficient maximum likelihood algorithm for phylogenetic tree reconstruction and an ultra-fast approximation for phylogenetic bootstrap. The package is available at the IQ-Tree homepage.

  • TREE-PUZZLE
    is a program package to reconstruct phylogenetic trees from protein, DNA, and binary data by maximum likelihood. The package is available at www.tree-puzzle.de.

  • IQPNNI (Important Quartet Puzzling with NNI Optimization)
    A quartet based method to reconstruct phylogenetic trees from really large datasets (DNA and protein). The method applies a QP-like approach requiring only a part of the quartets and some fast NNI optimization. The package is available at the IQPNNI homepage.

  • PDA (Phylogenetic Diversity Algorithm)
    implements efficient algorithms to solve the Phylogenetic Diversity (PD) problem. The package is available at the PDA homepage.

  • HGT
    A software to simulate and estimate Horizontal Gene Transfer events. The package is available at the HGT homepage.

  • TripleC
    a program to constuct consensus trees from rooted triples. The software is available at the TripleC homepage.





Next Generation Sequencing

  • NextGenMap (Next Generation Mapper)
    is a computer program to map NGS reads against a reference genome using CPUs or GPUs. The program is available at the NextGenMap homepage.

  • Teaser
    Teaser is a software package for optimizing NGS read mapping results. Through rapid automated benchmarks on simulated or real data sets, the most suitable mapper for an experiment can be found within minutes. By testing the same mapper on multiple parameter settings, results can be further tuned for accuracy or speed. At the end of each benchmark, Teaser presents the results in a browser-viewable report that includes interactive figures. The software is available at the Teaser homepage.

  • VARIFI
    Web-based Automatic Variant (SNPs and INDELs) Identification, Filtering and Annotation of Amplicon Sequencing Data. The tool is available at the VARIFI homepage.

  • NGC
    A compressor for high-throughput sequencing data. The package is available at the NGC homepage.

  • Bisulfite Sequencing Scrorer (BISS)
    is an analysis pipeline for the deep sequencing data after bisulfite conversion (BS-Seq). The package is available at the BiSS homepage.

  • MASon (Million Alignments in Seconds)
    is a C++ library that uses high performance architectures to reduce the computing time of NGS analysis pipelines. The program is available at the MASon homepage.

  • SNP2GO
    is an R package developed for the functional analysis of Genome-Wide Association (GWA) studies. The package is available at the SNP2GO homepage.

Phylogenetics :: Modelling

  • HaMSTR
    HaMSTR is a Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes. HaMSTR is accessible at www.deep-phylogeny.org/hamstr.

  • ImOSM (Imbed One Step Mutations into an alignment)
    A program to Imbed model violation as One Step Mutations into a sequence alignment. This is a useful tool to study the robustness in phylogeny inference. ImOSM homepage.

  • misfits
    is a computer program to evaluate the goodness of fit between a phylogenetic model and an alignment. The program is available at the misfits homepage.

  • ALIFRITZ
    performs statistical multiple alignment and phylogeny reconstruction simultaneously. The package is available at the ALIFRITZ homepage.

  • SISSI (Simulating Sequence Evolution with Site-Specific Interactions)
    SISSI is a software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices. The software is available at the SISSI homepage.

  • DupliDeli - Estimation of Gene Family Specific Duplication and Deletion Rates
    is a program to estimate gene family specific duplication and deletion rates as well as the ancestral number of gene copies. The package is available at the DupliDeli homepage.

  • RecDetec - detecting recombination and phylogenetic information along alignments RecDetec is a software to investigate recombination scenarios based on the bootscan principle along alignments of (viral) genomes. It also allowes to assess the content of phylogenetic information along alignments. The package is available at the RecDetec homepage.

  • REvolver: Modeling sequence evolution under domain constraints
    REvolver is a program to simulate protein sequence evolution. REvolver automatically integrates domain information described by a profile Hidden Markov Model (pHMM) into the simulation. The package is available at the REvolver homepage.

Miscellaneous

  • DAGwoman - DAG-based WOrkflow MANager
    is a workflow engine that allows running and managing DAG-based scientific workflows on computing resources. The package is available at the DAGwoman homepage.

  • EMOGEE (Estimator for MOdels of Gene Expression Evolution)
    implements neutral models for evolution of gene expression to analyze or simulate microarray data. EMOGEE and related tools are available at the EMOGEE homepage.

  • Epi-Speller
    is a program for analyzing multiple genome-wide profiling epigenomic data. The package is available at the Epi-Speller homepage

  • GeoMeTree (Geodesic Metric on Trees)
    GeoMeTree is a python program to compute the geodesic path between two phylogenetic trees. The package is available at the GeoMeTree homepage.

  • NGV (Next Generation Viewer)
    A Preprocessor and Browser for efficient display of large HTS Data Sets. The package is available at the NGV homepage.

  • TAXNAMECONVERT
    is a program to rename sequence and taxon names in tree and sequence files. The software is available at the Taxnameconvert homepage.

  • TreeSnatcher
    is a GUI-driven Java application that recognizes bifurcating and multifurcating trees in pixel images (like JPG) and outputs the tree in Newick format. The software is available at the TreeSnatcher homepage.

  • More

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