hyphaltip
I am a faculty member working primarily on fungal evolution using genomic tools. Development of comparative genomics and bioinformatics tools and training.
University of California-RiversideRiverside, CA
Pinned Repositories
cndtools
fork of cndtools
fungaltools
Misc scripts for fungal tools, mostly for use in papers
fungi-gene-prediction-params
Provide trained gene prediction parameters for Fungal genome annotation
gbrowse_conf_fungalgenomes
Supporting fungalgenomes.org website
genome-scripts
Genome Scripts used in fungal comparative genomics
htbda_perl_class
High Throughput Biological Data Analysis using Perl
mTEA
Mosquito TE Annotation
short-read-db
Database for shortreads and comparing overlap with genomic features
subopt-kaks
Suboptimal alignments and Ka, Ks calculations
Tutorial_GenomeEvolution
Genome Evolution Lecture for Phylogenomics Workshop
hyphaltip's Repositories
hyphaltip/gfftk
GFF toolkit
hyphaltip/KassonLab_PopGenomics_Nectriaceae_magnoliae
Nectriaceae magnoliae population genomics
hyphaltip/smudgeplot
Inference of ploidy and heterozygosity structure using whole genome sequencing data
hyphaltip/VCF-parser
GEN220 project
hyphaltip/adrian_chopchop
Example of how to setup Chop Chop runs
hyphaltip/amptk
Fungal ITS Clustering Package
hyphaltip/antismash
antiSMASH
hyphaltip/antismash_documentation
The antiSMASH online documentation
hyphaltip/bin3C
Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.
hyphaltip/bioconda-recipes
Conda recipes for the bioconda channel.
hyphaltip/BioCrust_Chihuahuan_PRJNA748083
Chihuahuan desert biocrust samples for PRJNA748083
hyphaltip/BioData_KEGG_decoder
bjtully - All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
hyphaltip/corason
Bioinformatic Tools for study Evolution of metabolic diversity
hyphaltip/CV
My CV
hyphaltip/dbcanLight
A lightweight rewrite of run_dbcan for better multithread performance
hyphaltip/DspikeIn
The importance of converting relative to absolute abundance in the context of microbial ecology: Introducing the user-friendly DspikeIn R package
hyphaltip/EDTA
Extensive de-novo TE Annotator
hyphaltip/find_ping_pong_JinfengPipeline
Directory for running Jinfeng's code for finding Ping. This directory is also found in the Rice_Rice_Baby team in the Stajich Lab github.
hyphaltip/Flye
De novo assembler for single molecule sequencing reads using repeat graphs
hyphaltip/fungalgenomes.org
FungalGenomes / Hyphaltip blog
hyphaltip/GToTree
A user-friendly workflow for phylogenomics
hyphaltip/impala
hyphaltip/kofam_scan
CLI tool to annotate genes with KOfam
hyphaltip/make_amptkdb_refseq
temp repo to make amptk libraries from ncbi refseq target loci
hyphaltip/methylmap
Methylmap is a tool for visualization of modified nucleotide frequencies for large cohort sizes.
hyphaltip/RelocaTE2
RelocaTE2
hyphaltip/relocate2_data_parsing
Project is designed around the manipulation of Relocate2 results. The goal is to have a place for code that is used to create combined insertion table.
hyphaltip/sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
hyphaltip/SpiecEasi
Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
hyphaltip/UHM_ITS_mucor_tree