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/htbda_perl_class
High Throughput Biological Data Analysis using Perl
hyphaltip/short-read-db
Database for shortreads and comparing overlap with genomic features
hyphaltip/mobedac-fungi
MOBeDAC Fungi Database
hyphaltip/pan-fungal-project
A Pan-Fungal Genomes Database
hyphaltip/CSHL_NGS
NGS DNA analysis for the CSHL 2012 Programming for Biology course
hyphaltip/macports
My local macports files
hyphaltip/PhyloSift
Phylogenetic and taxonomic analysis for genomes and metagenomes
hyphaltip/ucr-biocluster-scripts
UCR Biocluster job scripts
hyphaltip/bwa
Burrow-Wheeler Aligner
hyphaltip/ExaML
Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI
hyphaltip/H3K27
H3K27 neurospora project
hyphaltip/khmer
in-memory k-mer counting
hyphaltip/rhizobia-genomics
Scripts to support bacterial genomics project
hyphaltip/standard-RAxML
hyphaltip/TEamRice
Rice TE project
hyphaltip/Annocript
Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript to identify putative long non-coding RNAs among your transcripts.
hyphaltip/AoC15
Advent of Code 2015
hyphaltip/BINF_toolkit
Handy scripts for routine bioinformatic analysis
hyphaltip/biopython
Official git repository for Biopython (converted from CVS)
hyphaltip/fungidb-tools
Scripts to manage fungidb.org
hyphaltip/landslide
Generate a slideshow using the slides that power the html5-slides presentation
hyphaltip/MediaWiki-Extension--UserAdmin
UserAdmin is a MediaWiki extension which allows administrators to add and delete users, change user passwords, edit user details, edit user groups, resend emails (e.g. reset password email or welcome message email).
hyphaltip/parsnp
hyphaltip/planets
test planets
hyphaltip/RelocaTE
Find the locations of TEs using the TSD in unassembled short reads by comparing to a closely related reference genome assembly
hyphaltip/runnning_blast
Demo for Derreck
hyphaltip/SeqPrep
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
hyphaltip/trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
hyphaltip/vcflib
a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
hyphaltip/Workshop