Joseph F. Ryan

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

sowhat. Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)

FastqSifter. Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)

phylotocol. template, example, and instructions on how to make an a priori phylogenetic protocol

leapfrog. identify BLAST hits between two datasets by employing a third intermediate dataset

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.

2017-DEEPC_Ctenophora. HyPhy

matemaker. make artificial mate pairs from long sequences for scaffolding

DeBiasse_cnidophylogenomics. Perl

hmm2aln.pl. script to automate gene family phylogeny based using HMM

exoblast. compare genome assemblies using sequence similarity to transcript or protein sequences from a different species.

RyanLabUnixBestPractices. A set of conventions we use in our lab

SeaCucumberPhylogenomics. Sea cucumber phylogenomics

make_subalignment. This script takes a prefix of a subset of (our ingroup) taxa and will return an alignment of only those genes within the clade descended from the most recent common ancestor of all genes with the specified prefix.

tmppolar. temporary staging area for polar workshop update

RyanLabShortReadAssembly. Our pipeline for assembling short reads

ctenophore_innexins. Analyses of the innexins of ctenophores

2019-DeBiasse_etal_CorellaGenome. Corella genome project scripts, phylotocol, etc.

check_for_gold_in_short_seqs. Often before finalizing genome assemblies, short seqs are removed. This script uses transcripts to find bits missing in the long but present in the short. Note:GenBank requires removal of seqs shorter than 200.

SELECTINGS. A pipeline to detect positive Darwinian selection in large datasets

pal2nal_gblocker. produce a nucleotide alignment that corresponds with a GBLOCKED amino-acid alignment

2018-Pastrana_etal_SpongeParaHoxAnalyses. files related to testing for existance of sponge ParaHox genes

phyloconverge. an algorithm to look for convergent signals in phylogenetic trees

Steinworth_CnidarianHox. Cnidarian Hox Phylotocol and scripts

2018-Hernandez_and_Ryan_HGT. files associated w 2017 HGT study by Hernandez and Ryan

JFR-PerlModules. Perl extensions for dealing with molecular sequence data formats (FASTA, FASTQ, GFF3, and more)

Ohdera_et_al_2018. 3 Acraspeda genomes

2017b_Sasson_and_Ryan. A reconstruction of sexual modes throughout animal evolution

2017-Kayal_et_al. Shell