{"id":1420,"date":"2014-10-21T18:36:33","date_gmt":"2014-10-21T16:36:33","guid":{"rendered":"http:\/\/www.h-its.org\/?page_id=1420"},"modified":"2019-11-20T12:05:59","modified_gmt":"2019-11-20T11:05:59","slug":"software","status":"publish","type":"page","link":"https:\/\/www.h-its.org\/de\/forschung\/cme\/software\/","title":{"rendered":"Software"},"content":{"rendered":"\n
Software Phylogenetic Inference<\/a>
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RAxML<\/p>\n

Our standard tool for Maximum-likelihood based phylogenetic inference.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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ExaML<\/p>\n

Exascale Maximum Likelihood (ExaML): Code for extremely large-scale phylogenetic inference on supercomputers using MPI.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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Phylogenetic Likelihood Library<\/p>\n

Phylogenetic Likelihood Library: A highly optimized and parallized library for rapid prototyping and development of likelihood based phylogenetic inference codes.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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Perpetyally updating trees<\/p>\n

A pipeline that automatically updates reference trees using RAxML-Light when new sequences for the clade of interest appear on GenBank or …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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RAxML-Light<\/p>\n

A strapped down checkpointable RAxML version for computing huge trees on supercomputers. Development of this code has stopped, please use …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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Parsimonator<\/p>\n

A fast and simple open-source parsimony program for building phylogenies on DNA data.Hybrid MrBayes Parallelized Bayesian tree inference for large-scale …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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ExaBayes<\/p>\n

Parallelized Bayesian tree inference for large-scale datasets.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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llpll<\/p>\n

New, flexible low level phylogenetic likelihood library.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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RAxML next generation<\/p>\n

The all new, from scratch re-design of RAxML: better, faster, more scalable, easier to use.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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ModelTest next generation<\/p>\n

The all new faster ModelTest, superseding jModelTest and ProtTest.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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libpll-2<\/p>\n

Second version of libpll, including site repeats optimization.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n <\/div>\n\n <\/div>\n<\/div><\/div>\n\n\n\n

Phylogenetic Post-Analysis<\/a>
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Visual Tree Comparer<\/p>\n

A simple graphical tree comparison tool that visualizes differences between up to four different trees by highlighting the branches (bipartitions\/splits) …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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Tree Visualization Tool (very old)<\/p>\n

Old Tree visualization tool using treemaps and taxonomic information.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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AxParafit<\/p>\n

Highly optimized versions of Pierre Legendre\u2019s Parafit and DistPCoA programs for statistical analysis of host-parasite coevolution.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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Rogue Taxon Identification<\/p>\n

A new, scalable algorithm for rogue taxon identification.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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Dppdiv<\/p>\n

An optimized (using vector intrinsics) and parallelized version (using OpenMP) of the DPPDIV (original code by Tracy Heath) code for estimating …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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Phylogenetic Binning tool<\/p>\n

The code from the paper: S. Berger, R. L\u00fccking, A. Stamatakis on \u201cMorphology-based phylogenetic binning of the lichen genera Graphis …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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ForeSeqs<\/p>\n

Prediction of missing sequences and branch lengths on phylogenies inferred using MSAs that have missing\/gappy data.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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PTP<\/p>\n

A tool for delimiting species on phylogenies and evolutionary placements.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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MPTP<\/p>\n

A substantially faster, more scalable, and more accurate version of our PTP tool for single locus species delimitation<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n <\/div>\n\n <\/div>\n<\/div><\/div>\n\n\n\n

Next Generation Sequencing & Sequence Analysis<\/a>
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PEAR \u2013 Paired-End reAd mergeR<\/p>\n

An ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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GapMis<\/p>\n

A tool for flexible pairwise sequence alignment with a variable, but bounded, number of gaps.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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libgapmis<\/p>\n

An ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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genesis<\/p>\n

A toolkit for working with phylogenetic data, mainly for evolutionary placements of short NGS reads on a reference phylogenetic tree. The …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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Evolutionary Placement Algorithm<\/p>\n

Algorithm for placing short reads onto a given reference phylogeny. This is part of standard RAxML.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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PaPaRa<\/p>\n

PArsimony-based Phylogeny-Aware Read alignment program. The tool uses a given multipe sequence alignment and corresponding reference tree to align short reads …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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MoTeX<\/p>\n

An accurate and efficient tool for MoTif eXtraction.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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ChromatoGate<\/p>\n

A tool for analyzing and editing\/correcting chromatogram data.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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SATIVA<\/p>\n

Semi-Automatic Taxonomy Improvement and Validation Algorithm. Identifies taxonomically mislabeled sequences and suggests corrections using EPA (Evolutionary Placement Algorithm).<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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EPA next generation<\/p>\n

Stand-alone, much faster, and massively parallel re-implementation of the Evolutionary Placement Algorithm.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n <\/div>\n\n <\/div>\n<\/div><\/div>\n\n\n\n

Population Genetics<\/a>
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AnA-FiTS<\/p>\n

A very fast forward-in-time simulator for population genetics.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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Sweed<\/p>\n

A parallel and checkpointable tool that implements a composite likelihood ratio test for detecting selective sweeps. SweeD is based on the …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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OmegaPlus<\/p>\n

A parallel tool for rapid & scalable detection of selective sweeps in whole-genome datasets using the omega statistic.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n <\/div>\n\n <\/div>\n<\/div><\/div>\n\n\n\n

Web Services<\/a>
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RAxML-Light Web-Service<\/p>\n

Available at the San Diego Supercomputer Center (supported by the NSF iPlant collaborative) To use this service you will first need …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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WEB-Servers for evolutionary placement of short reads<\/p>\n

Our basic serverFancy Swiss Server<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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Rogue Taxon Identification Web-Server<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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PTP Web-Service<\/p>\n

Access the web server for species delimitation using our new PTP method.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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RAxML Web Servers<\/p>\n

Vital IT unit of the Swiss Institute of BioinformaticsCIPRES portal at San Diego Supercomputer CenterNew beta-version of the CIPRES portal&…<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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MPTP Web Server<\/p>\n

Access the new species delimitation web service using the new mptp approach.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n <\/div>\n\n <\/div>\n\n\n\n

<\/p>\n<\/div><\/div>\n\n\n\n

Miscellaneous<\/a>
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Microbenchmark for Denormalized Floating Point Numbers<\/p>\n

A small benchmark code, mainly for teaching purposes that can be used to highlight the performance impact of de-normalized floating point …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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Reconfigurable Architectures (FPGAs)<\/p>\n

Reconfigurable architectures for Bioinformatics applications designed by our former lab member Dr. Nikos Alachiotis.<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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File conversion scripts<\/p>\n

Shell script for fasta to phylip conversion.Matlab programs by Lowie Li for fasta to phylip and&…<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n

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TreeCounter<\/p>\n

Small program to compute the number of possible rooted and unrooted binary trees for n taxa or to compute the number …<\/p>\n Mehr erfahren<\/a>\n <\/div>\n \n <\/div>\n\n <\/div>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":3,"featured_media":40636,"parent":46,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"page-templates\/group.php","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"hits-research-group":[1282],"class_list":["post-1420","page","type-page","status-publish","has-post-thumbnail","hentry","hits-research-group-cme-de"],"acf":[],"yoast_head":"\nSoftware - HITS gGmbH<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.h-its.org\/de\/forschung\/cme\/software\/\" \/>\n<meta property=\"og:locale\" content=\"de_DE\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Software - 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