A program that is a variant of the Minimum χ2 (MC) method for limiting dilution assays.
It allows the user to specify the probabilities of a false negative and false positive PCR
(it is also a tool for the quantitation of ampliable viral templates, i.e., viral load
under the conditions of your assay). The program is available either as a java applet
that can be run via the web or as a program that can be downloaded and run locally.
A scoring tool that allows users to analyze V3 loop coreceptor motifs.
A BLAST web server that allows users to search multiple sequence databases including public and local databases.
A web server to analyze phylogenies, sequence divergence, diversity and informative sites.
A web database to store, retrieve and analyze HIV immunology data (ELISpot, HLA, etc.).
A web database to store, search and retrieve lab used HIV primers.
A web service to track scientific literatures via user-specified journals and keywords.
A test for the detection of latent reservoirs.
A test for the detection of continued viral replication under antiviral therapies.
A tool to pull branch lengths from newick tree and returns divergence and diversity.
An Excel spreadsheet that jitters points with identical (x, y) values.
- PAUP* Diversity Matrix Formatter A tool to reformat diagonal distance matrices into columnar output.
- UniSeq A tool to identify and extract unique sequences
- ChromatQuantitator A tool to quantitate mixed base composition in Sanger sequencing chromatograms.
- Viral Growth Rate Calculation A tool for comparing and evaluating competitive viral fitness.
- Sequence Name Reformatter A tool to reformat sequence names in a sequence fasta file.
- Explain Phred — A quick Phred+33 quality score explainer
- Integration Sites A bioinformatics tool
used to define the location of HIV integration sites in the human genome.
Perl scripts and libraries
- ICC A software pipeline to analyze next-generation sequencing data (454 pyrosequencing, Ion Torrent, etc.), including read quality filtering and alignment, indel and carryforward error correction, single nucleotide variant calling, and calculation of nucleotide variant and hyplotype frequencies
- CorQ A software pipeline of quality score based identification and correction of 454 pyrosequencing errors.
- DiverAnalysis.pl command-line analysis of sequence divergence and diversity
- AutoSequin.pl automatically annotate sequences for bulk submission to GenBenk
- NetNGlycParser.pl reformat output from NetNLGlyc
- NetOGlycParser.pl reformat output from NetOLGlyc
- ChangeNewickNodeId.pl relabel nodes in a Newick tree
- CountAAFreq.pl calculate amino acid frequency for each position in an alignment
- RemoveOverlapSeq.pl remove identical and overlapping sequences from an alignment
- SequLocatorParser.pl reformat output from LANL's sequence locator
- Sequence manipulator format conversion between alignment formats, fasta sequence cleaner
- NewickTermBranch.pl report external branch lengths of a Newick tree.
- ColumnDist2diverstest.pl refomat column distance matrix into the input format of diverstest web tool
- parseBlastXML_calcFreq.pl calculate nucleotide frequencies at each position of reference sequence from a BLASTn xml output file
- parseBlastXML_calcErrRate.pl calculate error rates of different types (insertion, deletion and substitution) from a BLASTn xml output file
- App::RecordStream::Bio - A collection of record-handling tools related to biology, for use with the excellent data-slicing tools in App::RecordStream
- Bio::WebService::LANL::SequenceLocator - A Perl library providing programmatic access to LANL's sequence locator tool, used to provide our sequence locator JSON web API
For a complete list of services please visit the CFAR Molecular Profiling and Computational Biology core web page
These tools were developed in part with funding from the University of Washington Center for AIDS Research (CFAR), an NIH funded program under award number P30AI027757
which is supported by the following NIH Institutes and Centers (NIAID, NCI, NIMH, NIDA, NICHD, NHLBI, NIA).