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/fungi-gene-prediction-params
Provide trained gene prediction parameters for Fungal genome annotation
hyphaltip/Tutorial_GenomeEvolution
Genome Evolution Lecture for Phylogenomics Workshop
hyphaltip/GEN220_2015
GEN220 course, Fall 2015 edition
hyphaltip/ASTRAL
Accurate Species TRee ALgorithm
hyphaltip/Binning
Scripts required to calculate tetramer frequencies and create input files for ESOM. See: Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10: R85
hyphaltip/canu
A single molecule sequence assembler for genomes large and small.
hyphaltip/CNVnator
a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
hyphaltip/cocci_repeats
Coccidioides repeat analysis
hyphaltip/coding_challenge
coding challenge
hyphaltip/Contentious_relationships_Code
Code from Shen et al Nat Eco Evo 2017
hyphaltip/disopred
Protein structural disorder prediction
hyphaltip/EukCC
Tool to estimate genome quality of microbial eukaryotes
hyphaltip/Gap2Seq
Gap2Seq is a gap filling and insertion genotyping tool.
hyphaltip/gene2product
Curated list of gene names and product descriptions that pass NCBI genome submission rules.
hyphaltip/ggtree-book
:book:The ggtree book
hyphaltip/got_pubmed
Retrieve pubmed IDs for resources
hyphaltip/homebrew-science
:snowflake: Scientific formulae for Homebrew and Linuxbrew (legacy)
hyphaltip/kallisto
Near-optimal RNA-Seq quantification
hyphaltip/Massospora_genomes
hyphaltip/masurca
hyphaltip/npScarf
hyphaltip/Personal-NGS-Cloud
hyphaltip/PopPUNK
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
hyphaltip/R-genomics
Lesson on data analysis and visualization in R for genomics
hyphaltip/redundans
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
hyphaltip/SolidBin
A genome binning method for contig binning, based on semi-supervised spectral clustering method.
hyphaltip/systemPipeRdata
NGS workflow templates and sample data
hyphaltip/test_gen220_fun
hyphaltip/ucr-hpcc.github.io
UCR Research Computing Facility
hyphaltip/VAPiD
VAPiD: Viral Annotation and Identification Pipeline