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    • Perl
      0000Updated Dec 13, 2024Dec 13, 2024
    • Adapting PORPIDPipeline to use Indexed PacBio reads rather than sample ID
      Julia
      MIT License
      0000Updated Oct 17, 2024Oct 17, 2024
    • Perl
      0000Updated Sep 27, 2024Sep 27, 2024
    • phylobook

      Public
      JavaScript
      Other
      2200Updated Sep 10, 2024Sep 10, 2024
    • HIV-1 Reservoirs Integration Sites
      Python
      Other
      0000Updated Sep 9, 2024Sep 9, 2024
    • Import tool for Django
      Python
      0000Updated Sep 9, 2024Sep 9, 2024
    • For demultiplexing and creating consensus from Indexed PacBio reads from SGA PCR.
      Jupyter Notebook
      MIT License
      0000Updated Jul 1, 2024Jul 1, 2024
    • Python
      0000Updated Jun 18, 2024Jun 18, 2024
    • A program pipeline to run through multiple programs from sequence alignment fasta file to the resuts ready to publish on phylobook server
      Python
      Other
      1110Updated Jun 10, 2024Jun 10, 2024
    • Python
      0200Updated Apr 27, 2024Apr 27, 2024
    • ViroBLAST standalone package
      Perl
      101530Updated Apr 4, 2024Apr 4, 2024
    • Python
      5000Updated Sep 28, 2023Sep 28, 2023
    • Python script to collapse sequences into unique sequences
      Python
      1000Updated Sep 13, 2023Sep 13, 2023
    • This is a repository of R code that clusters sequence data using the GAP procedure and K-mediods clustering. The input is a folder containing fastA files for all the data within a project. The output is a collection of files containing the sequence-to-cluster-ID for each clustering run (e.g. the GAP procedure, and various K's in K-mediod cluster…
      R
      MIT License
      0000Updated Sep 12, 2023Sep 12, 2023
    • creates sUMI and dUMI output files and consensus sequences from PacBio sequencing data
      Julia
      0000Updated Feb 23, 2023Feb 23, 2023
    • snakemake pipeline to demultiplex PacBio reads using Index sequences added during PCR
      Julia
      0000Updated Feb 23, 2023Feb 23, 2023
    • viroverse

      Public
      a platform for the collection, storage, retrieval, and analysis of experimental data for laboratory workflows
      Perl
      MIT License
      15356Updated Dec 9, 2022Dec 9, 2022
    • Automate LANL's HIV mutation-highlighting tool
      Python
      MIT License
      1100Updated Sep 23, 2022Sep 23, 2022
    • R scripts used in publication: Genomic changes in Kaposi Sarcoma-associated Herpesvirus and their clinical correlates
      R
      0000Updated Aug 27, 2022Aug 27, 2022
    • Bio-Cigar

      Public
      Parse CIGAR strings and translate coordinates to/from reference/query
      Perl
      Other
      3620Updated Jun 28, 2022Jun 28, 2022
    • A toolkit to perform phylogenetic analysis via PhyML_v3.3 and produce the pairwise distances
      Python
      0000Updated May 11, 2022May 11, 2022
    • FigTree modified with more command line configuration options. For use in pipelines/automation.
      Java
      0000Updated Mar 21, 2022Mar 21, 2022
    • A software pipeline to process HIV V3 sequences via Illumina MiSeq for the viral tropism analysis
      Perl
      0000Updated Mar 11, 2022Mar 11, 2022
    • Shell scripts to create a consistent data workflow using PORPID-postproc
      Shell
      0000Updated Dec 16, 2021Dec 16, 2021
    • A workflow and toolkit of perl scripts to manipulate multiple sequence alignments
      Perl
      4100Updated May 25, 2021May 25, 2021
    • A workflow and toolkit of perl scripts for selecting rev-env variants for synthesis
      Perl
      0000Updated Dec 7, 2020Dec 7, 2020
    • A generic component for maintaining the sort state of a set of sortable fields, e.g. table columns.
      JavaScript
      0000Updated Aug 6, 2020Aug 6, 2020
    • A bridge between File objects and your AngularJS components
      0000Updated Aug 6, 2020Aug 6, 2020
    • A minimal file upload widget wrapping standard file inputs with drag-and-drop behaviour
      JavaScript
      0000Updated Aug 6, 2020Aug 6, 2020
    • Python
      Other
      0000Updated Apr 6, 2020Apr 6, 2020