Web tools

• QUALITY  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.
• PSSM  A scoring tool developed by Mark Jensen and other lab members that allows users to analyze V3 loop coreceptor motifs.
• ViroBLAST  A BLAST web server that allows users to search multiple sequence databases including public and local.
• Diver  A web interface to analyze sequence divergence and diversity (note: this tool does not work with Internet Explorer; please use Firefox or Safari).
• EpitopeDB  A web database to store, retrieve and analyze HIV immunology data (ELISpot, HLA, etc.).
• PrimerDB  A web database to store, search and retrieve PCR and sequencing primers specific to HIV (collection from Mullins lab).
• LiteraTracker  A web service to track scientific literature.
• COTree  A web interface that re-roots a newick tree at the least squares point (COT).
• DistParser  A tool to extract branch lengths from newick trees. It returns divergence and diversity values.
• JitterCalc  An Excel spreadsheet that jitters points with identical (x, y) values, i.e., it allows a user to jitter data symbols along the X-axis so that the symbols no longer completely overlap.

Perl scripts

• DiverAnalysis.pl   A program to perform phylogenetic analysis of sequence divergence and diversity.
• AutoSequin.pl   A program to speed the process of submitting HIV sequences to GenBank via NCBI's Sequin program.
• NetNGlycParser.pl   A program to parse the output of NetNGlyc 1.0 Server that predicts N-Glycosylation sites
• NetOGlycParser.pl   A program to parse the output of NetOGlyc 3.1 Server that produces neural network predictions of mucin type GalNAc O-glycosylation sites
• ChangeNewickNodeId.pl   A program that manipulates a newick tree by replacing the tree node identifiers with new identifiers that are defined in a file.
• CountAAFreq.pl   A program to calculate amino acid frequencies at each position of a set of aligned amino acid sequences.
• RemoveOverlapSeq.pl   A program to check a set of sequences and remove identical sequences and overlapped short sequences.
• SequLocatorParser.pl   A program to parse the output of LANL's HIV/SIV Sequence Locator Tool
• Sequence manipulator   A collection of sequence manipulating scripts, including sequence cleaning and sequence format conversion.
  • List2Fasta.pl
  • Nexus2Fasta.pl
  • ASN2Fasta.pl
  • SwissProt2Fasta.pl
  • SequCleaner.pl

SMS2

• (a local port of Paul Stothard's Sequence Manipulation Package (note: these tools do not work with Internet Explorer or Safari; please use Firefox)