jphmm.gobics.de

hiv.lanl.gov

Sequence Alignments

http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html

Index of all tools. Are nucleotide and protein alignments that represent the fullest spectrum of sequences in the database. Are a filtered subset of sequences from the HIV-1 web alignments. Contain approximately 4 representatives of each subtype. Are the subset of sequences printed in the HIV Sequence Compendium. Include a consensus for each subtype, an M-group consensus-of-consensuses, and some ancestral sequences. Before use, please read the additional information below. Pre-defined region of the genome.

hiv.lanl.gov

HIV Sequence Database: OLD NEWS

http://www.hiv.lanl.gov/components/news/old_news.html

Index of all tools. News releases from the LANL HIV Databases are available as RSS feeds. Immune Epitope Database User Workshop October 24 - 25, 2016. The IEDB is an NIH-supported, freely available resource that provides access to published data related to antibody and T cell epitopes, as well as online tools for prediction and further analysis of immune epitopes. A HIV Database. HIV Sequence Compendium 2016. HIV Sequence Compendium 2016. Is now available online. Tool provides a graphical view of sequenc...

hiv.lanl.gov

HIV Circulating Recombinant Forms (CRFs)

http://www.hiv.lanl.gov/content/sequence/HIV/CRFs/CRFs.html

Index of all tools. HIV Circulating Recombinant Forms (CRFs). This page presents an overview of existing circulating recombinant forms (CRFs). We also provide a page listing CRF Breakpoints. If you find an inaccuracy, please contact us. For information about subtype and CRF naming, see Nomenclature. New CRFs will be numbered sequentially as they become known to us. The Recombinant HIV-1 Drawing Tool. Provides a handy way to produce a quality drawing of your CRFs and URFs. KP Ng and K.K. Tee. CRF02, B, G.

gobics.de

gobics.de: Software

http://gobics.de/department/software

University of Göttingen. Faculty of Biology and Psychology. Institute of Microbiology and Genetics. Software tools available through GOBICS (GÃ ttingen Bioinformatics Compute Server):. Alignment free sequence comparison. A web-server for fast comparative functional profiling of metagenomes. Gene prediction for eukaryotes. Ultra-fast functional profiling of large protein sequence collections. Clustering and Visualization of Metabolic Markers. Multiple sequence alignment; various program versions available.

hiv.lanl.gov

FindModel input

http://www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html

Index of all tools. FindModel analyzes your alignment to see which phylogenetic model best describes your data; this model can then be used to generate a better tree. Finding the best evolutionary model is computationally intensive, so we limit default runs to a reduced set. Of 12 models, excluding those that do not have an obvious biological interpretation. (If you know of any system where Modeltest consistently returns a model that we do not include, please let us know.) The full set. Set and 350 Kb.

hiv.lanl.gov

CATNAP: Hybrid

http://www.hiv.lanl.gov/components/sequence/HIV/neutralization/hybrid.comp

Index of all tools. Compile, Analyze and Tally NAb Panels. Data for HIV-1 Env neutralization with published data. Paste or upload assay data. Or example files (.zip). Virus sequence alignment of your assay. Use your own HIV-1 ENV alignment (HXB2 must be included). See alignment file requirements. Or example files (.zip). Use LANL HIV-1 Env alignment. Virus accessions must be provided in the assay csv file). Database assays for the same antibodies in your data file. Add assays for additional antibodies.

hiv.lanl.gov

HIV Database Editors

http://www.hiv.lanl.gov/content/sequence/HIV/editors.html

Index of all tools. Last modified: Thu Jun 27 12:00 2013. Contact us at seq-info@lanl.gov. Operated by Los Alamos National Security, LLC, for the U.S. Department of Energy's. National Nuclear Security Administration.

hiv.lanl.gov

HIV sequence database main page

http://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html

Index of all tools. Retrieves HIV and SIV sequences, which can then be aligned and used to build trees. Retrieves HIV sequences based on geographical distribution. Uses jBrowse to display diverse data about the HIV-1 genome and proteome. Tools for working with sequences. Lists all our online tools, organized by function. Includes Consensus and Ancestral Sequences, Subtype Reference Alignments, and Complete Alignments. Print or order our annual publication. Tutorials and other information. Tool provides q...

hiv.lanl.gov

PCOORD Interface

http://www.hiv.lanl.gov/content/sequence/PCOORD/PCOORD.html

Index of all tools. PCOORD (Principal Coordinate Analysis) is a procedure to find meaningful patterns in sequence data. This tool attempts to automatically recognize the format of your input file. If this fails, you can use our Format Converter. Paste your input here. Or upload your file. Select distance matrix type. Last modified: Thu Jan 21 14:09 2016. Contact us at seq-info@lanl.gov. Operated by Los Alamos National Security, LLC, for the U.S. Department of Energy's.