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    66 repositories

    • V706_alignment_process

      Public
      An alignment pipeline for HVTN706 study
      Python
      •0•0•0•0•Updated Mar 11, 2026Mar 11, 2026

    • NatComm_scripts

      Public
      Python
      •0•0•0•0•Updated Mar 8, 2026Mar 8, 2026

    • sequence_collapsing

      Public
      Python script to collapse sequences into unique sequences
      Python
      •3•0•0•0•Updated Jan 16, 2026Jan 16, 2026

    • FUBAR_in_batch

      Public
      A Python script for running FUBAR (Fast Unconstrained Bayesian AppRoximation for inferring selection) analysis on sequence codon alignment files in batch
      Python
      •0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • MullinsLab.github.io

      Public
      MullinsLab WebSite
      HTML
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • phylobook_pipeline

      Public
      A program pipeline to run through multiple programs from sequence alignment fasta file to the resuts ready to publish on phylobook server
      Python
      •
      Other
      •2•1•1•0•Updated Jul 14, 2025Jul 14, 2025

    • ML_Import_Wizard

      Public
      Import tool for Django
      Python
      •1•0•0•0•Updated Jun 5, 2025Jun 5, 2025

    • HIV_hybrid_transcript

      Public
      Perl
      •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • PORPIDpipeline-index-primers

      Public
      Adapting PORPIDPipeline to use Indexed PacBio reads rather than sample ID
      Julia
      •
      MIT License
      •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • Illumina_IS_BP

      Public
      Perl
      •0•0•0•0•Updated Sep 27, 2024Sep 27, 2024

    • phylobook

      Public
      JavaScript
      •
      Other
      •2•2•0•1•Updated Sep 10, 2024Sep 10, 2024

    • HIRIS_project

      Public
      HIV-1 Reservoirs Integration Sites
      Python
      •
      Other
      •0•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • sga_index_consensus

      Public
      For demultiplexing and creating consensus from Indexed PacBio reads from SGA PCR.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 1, 2024Jul 1, 2024

    • ML_Export_Wizard

      Public
      Python
      •0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • Highlighter

      Public
      Python
      •1•4•0•0•Updated Apr 27, 2024Apr 27, 2024

    • ViroblastStandalone

      Public
      ViroBLAST standalone package
      Perl
      •10•16•3•0•Updated Apr 4, 2024Apr 4, 2024

    • Sequence_alignment_process

      Public
      Python
      •5•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • ClusteringForPhylobook

      Public
      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 a…
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 12, 2023Sep 12, 2023

    • sUMI_dUMI_comparison

      Public
      creates sUMI and dUMI output files and consensus sequences from PacBio sequencing data
      Julia
      •0•0•0•0•Updated Feb 23, 2023Feb 23, 2023

    • chunked_demux

      Public
      snakemake pipeline to demultiplex PacBio reads using Index sequences added during PCR
      Julia
      •0•0•0•0•Updated Feb 23, 2023Feb 23, 2023

    • viroverse

      Public
      a platform for the collection, storage, retrieval, and analysis of experimental data for laboratory workflows
      laboratorywebappmicrobiology
      laboratorywebappmicrobiologyhiv
      Perl
      •
      MIT License
      •1•6•35•6•Updated Dec 9, 2022Dec 9, 2022

    • highlighter_bot

      Public
      Automate LANL's HIV mutation-highlighting tool
      Python
      •
      MIT License
      •1•1•0•0•Updated Sep 23, 2022Sep 23, 2022

    • HHV8-non-B-DNA

      Public
      R scripts used in publication: Genomic changes in Kaposi Sarcoma-associated Herpesvirus and their clinical correlates
      R
      •0•0•0•0•Updated Aug 27, 2022Aug 27, 2022

    • Bio-Cigar

      Public
      Parse CIGAR strings and translate coordinates to/from reference/query
      Perl
      •
      Other
      •3•6•2•0•Updated Jun 28, 2022Jun 28, 2022

    • run_phyml_batch

      Public
      A toolkit to perform phylogenetic analysis via PhyML_v3.3 and produce the pairwise distances
      Python
      •0•0•0•0•Updated May 11, 2022May 11, 2022

    • figtree-enhanced-command-line

      Public
      FigTree modified with more command line configuration options. For use in pipelines/automation.
      Java
      •0•0•0•0•Updated Mar 21, 2022Mar 21, 2022

    • MiSeq_viral_tropism

      Public
      A software pipeline to process HIV V3 sequences via Illumina MiSeq for the viral tropism analysis
      Perl
      •0•0•0•0•Updated Mar 11, 2022Mar 11, 2022

    • PORPID_helper_scripts

      Public
      Shell scripts to create a consistent data workflow using PORPID-postproc
      Shell
      •0•0•0•0•Updated Dec 16, 2021Dec 16, 2021

    • AMP_alignment_process

      Public
      A workflow and toolkit of perl scripts to manipulate multiple sequence alignments
      Perl
      •4•1•0•0•Updated May 25, 2021May 25, 2021

    • AMP-pl-variant-selection

      Public
      A workflow and toolkit of perl scripts for selecting rev-env variants for synthesis
      Perl
      •0•0•0•0•Updated Dec 7, 2020Dec 7, 2020
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