Joseph F. Ryan's repositories
estimate_genome_size.pl
Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
alien_index
identify potential non-animal transcripts in animal transcriptomes
FastqSifter
Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)
Hernandez_Ryan_2021_Recoding
Simulation study of recoding effectiveness
hmm2aln.pl
script to automate gene family phylogeny based using HMM
SeaCucumberPhylogenomics
Sea cucumber phylogenomics
ctenophore_innexins
Analyses of the innexins of ctenophores
RyanLabShortReadAssembly
Our pipeline for assembling short reads
SELECTINGS
A pipeline to detect positive Darwinian selection in large datasets
Steinworth_CnidarianHox
Cnidarian Hox Phylotocol and scripts
2019-Babonis_et_al_trypsins
Files corresponding with Trypsin study by Babonis et al.
bioconda-recipes
Conda recipes for the bioconda channel.
Bryozoa_innexin
phylogenetic analysis of lophotrochozoa innexins with a focus on the evolution of bryzoan innexins
Cnidaria_shaker_channels
phylogenetic analyses of shaker K+ channels from Cnidaria
DendroPerl
Port of DendroPy to Perl
JFR-PerlModules
Perl extensions for dealing with molecular sequence data formats (FASTA, FASTQ, GFF3, and more)
Leys_et_al_Ephydatia_cell_atlas
Analyses from Leys et al. - An atlas of morphology of the freshwater sponge Ephydatia muelleri
Nematostella_DKK
Analysis of DKK genes in Nematostella vectensis
no_transcript_left_behind
use transcriptome to build haplotig-merged assembly