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2017-deepc_ctenophora

2017-kayal_et_al

2017b_sasson_and_ryan

A reconstruction of sexual modes throughout animal evolution

2018-babonis_et_al_ryan

Supplemental information from: Babonis et al. 2018 "Integrating embryonic..."

2018-hernandez_and_ryan_hgt

files associated w 2017 HGT study by Hernandez and Ryan

2018-pastrana_etal_spongeparahoxanalyses

files related to testing for existance of sponge ParaHox genes

2018_genecontentsim

Planned analyses for evaluating the effect of transcriptomic data on gene content simulations

2018_sasson_jacquez_ryan

2019-babonis_et_al_trypsins

Files corresponding with Trypsin study by Babonis et al.

2019-debiasse_etal_corellagenome

Corella genome project scripts, phylotocol, etc.

alien_index

identify potential non-animal transcripts in animal transcriptomes

almazan_et_al_auricles_regen

beroe_genome

bioconda-recipes

Conda recipes for the bioconda channel.

bryozoa_innexin

phylogenetic analysis of lophotrochozoa innexins with a focus on the evolution of bryzoan innexins

ceriantharia_phylogenomics

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.

chet

Produces an index (chet index) of compositional heterogeneity for 2 clades

cnidaria_shaker_channels

phylogenetic analyses of shaker K+ channels from Cnidaria

ctenophore_innexins

Analyses of the innexins of ctenophores

dayhoffrecodingtests

exploration of dayhoff recoding

debiasse_cnidophylogenomics

dendroperl

Port of DendroPy to Perl

doliolid_gegenbauri_phylogenomics

estimate_genome_size.pl

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

exoblast

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

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

holothuria_glaberrima_draft_genome

Holothuria glaberrima genome project scripts, commands, data, phylotocol, etc.