Pinned Repositories
454-filter
Simple and FAST barcode splitter for 454 FASTA files.
BUSTED-SRV
The effect of synonymous rate variation on BUSTED
gb_taxonomy_tools
GenBank taxonomy processing tools
HIVClustering
hyphy-support
Examples/patches etc created in response to HyPhy issues
IgSCUEAL
B-cell 454 processing
pubs
Scripts and data for group publications
SARS-CoV-2-variation
SCUEAL
SCUEAL Batch Files
spond's Repositories
spond/gb_taxonomy_tools
GenBank taxonomy processing tools
spond/IgSCUEAL
B-cell 454 processing
spond/hyphy-support
Examples/patches etc created in response to HyPhy issues
spond/pubs
Scripts and data for group publications
spond/SARS-CoV-2-variation
spond/BUSTED-SRV
The effect of synonymous rate variation on BUSTED
spond/CV.js
D3/Bootstrap CV generator
spond/TestForPositiveSelection
spond/alignment-tutorial-js
spond/BioExt
A few handy bioinformatics tools not already within BioPython
spond/course-description.js
Simple D3/Bootstrap based course description pages
spond/d3-array
Array manipulation, ordering, searching, summarizing, etc.
spond/hivclustering-1
spond/hivtrace
spond/hivtrace-viz
spond/hyphy
HyPhy: Hypothesis testing using Phylogenies
spond/hyphy-gui
Desktop application for HyPhy
spond/hyphy-vision
Visualize HyPhy results in your browser
spond/IAV-H3N2-analysis
Comparative analysis of H3N2 human/avian/mammalian isolates.
spond/layout-phylotree
layout.phylotree
spond/libtn93
C library to compute Tamura-Nei distances between (nucleotide) strings
spond/misc
spond/MNM_SelectionTests
Tests of selection incorporating multinucleotide mutations
spond/phylotree.js
Interactive viewer of phylogenetic trees
spond/PolEvolution
HyPhy scripts to perform multi-patient rate analyses on longitudinal pol isolates
spond/SARS-CoV-2
spond/SARS-CoV-2-clade-analysis
spond/SequenceComparison
spond/talks
Various Talks/Presentations
spond/tools-iuc
Tool Shed repositories maintained by the Intergalactic Utilities Commission