Pinned Repositories
2017-DEEPC_Ctenophora
alien_index
identify potential non-animal transcripts in animal transcriptomes
estimate_genome_size.pl
Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
FastqSifter
Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)
Hernandez_Ryan_2021_Recoding
Simulation study of recoding effectiveness
isoblat
use RNA transcripts to assess assembly - this program parses the output of a BLAT run of transcriptome vs. a genome. It returns 1) Total % mapped, 2) average %coverage of a mapping, and 3) number of transcripts mapping to a single contig/scaffold. It is simple to run. Just run the blat (transcripts vs. genome) and then run the script with the blat-output and your transcript-fasta-file as arguments.
leapfrog
identify BLAST hits between two datasets by employing a third intermediate dataset
matemaker
make artificial mate pairs from long sequences for scaffolding
phylotocol
template, example, and instructions on how to make an a priori phylogenetic protocol
sowhat
Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)
josephryan's Repositories
josephryan/estimate_genome_size.pl
Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
josephryan/alien_index
identify potential non-animal transcripts in animal transcriptomes
josephryan/sowhat
Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)
josephryan/FastqSifter
Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)
josephryan/Hernandez_Ryan_2021_Recoding
Simulation study of recoding effectiveness
josephryan/matemaker
make artificial mate pairs from long sequences for scaffolding
josephryan/hmm2aln.pl
script to automate gene family phylogeny based using HMM
josephryan/SeaCucumberPhylogenomics
Sea cucumber phylogenomics
josephryan/ctenophore_innexins
Analyses of the innexins of ctenophores
josephryan/DeBiasse_cnidophylogenomics
josephryan/RyanLabShortReadAssembly
Our pipeline for assembling short reads
josephryan/SELECTINGS
A pipeline to detect positive Darwinian selection in large datasets
josephryan/Steinworth_CnidarianHox
Cnidarian Hox Phylotocol and scripts
josephryan/tmppolar
temporary staging area for polar workshop update
josephryan/Ceriantharia_phylogenomics
josephryan/RyanLab
Repository for supplementary materials produced by the Ryan Lab
josephryan/2019-Babonis_et_al_trypsins
Files corresponding with Trypsin study by Babonis et al.
josephryan/Almazan_et_al_auricles_regen
josephryan/Beroe_genome
josephryan/bioconda-recipes
Conda recipes for the bioconda channel.
josephryan/Bryozoa_innexin
phylogenetic analysis of lophotrochozoa innexins with a focus on the evolution of bryzoan innexins
josephryan/Cnidaria_shaker_channels
phylogenetic analyses of shaker K+ channels from Cnidaria
josephryan/DendroPerl
Port of DendroPy to Perl
josephryan/Doliolid_gegenbauri_phylogenomics
josephryan/JFR-PerlModules
Perl extensions for dealing with molecular sequence data formats (FASTA, FASTQ, GFF3, and more)
josephryan/Leys_et_al_Ephydatia_cell_atlas
Analyses from Leys et al. - An atlas of morphology of the freshwater sponge Ephydatia muelleri
josephryan/Nematostella_DKK
Analysis of DKK genes in Nematostella vectensis
josephryan/no_transcript_left_behind
use transcriptome to build haplotig-merged assembly
josephryan/polar_workshop_scripts
josephryan/SpezHox
Analyses of the Hox genes of the Sea Urchin Echinometra sp. EZ