Castoe Lab
Department of Biology
University of Texas Arlington
Lab Links
Genomics Working Group Websites
Snake Genomics Genome10K Crocodile Genomics
Collaborators’ Websites
David Pollock (U Colorado Med School) - Evolutionary Genomics and Protein Evolution)
AP Jason de Koning (Univ. Calgary Med School - Evolutionary Genomics and Protein Evolution)
Sam Fox (Oregon State-Transcriptomics)
Peter Uetz (Virginia Commonwealth University - Protein Interactions, Reptile Taxonomy and Genomics)
Steve Mackessy (U Northern Colorado - Snake venom biochemistry and evolution)
Stephen Secor (U Alabama - Comparative physiology)
David Ray (Mississippi State U - Crocodilian genomics)
Juan Manuel Daza (U. Antiochia, Medellin, Colombia - Reptile systematics and evolution)
Jonathan Campbell (UTA - Herpetology)
Matthew Fujita (UTA - Herpetology and Comparative Genomics)
Eric N Smith (UTA - Herpetology and Systematics)
Paul Chippindale (UTA - Herpetology and Systematics)
Scientific Software Links
Oligonucleotide design
-IDT oligo design
DNA/Protein Alignment
-Clustal
-Mega
-PRANK
Phylogenetic Analysis
-Beast
-MrBayes
-nhPhyML (analysis with non-stationary non-homomogenous models, and ancestral GC estimation)
-Tracer
-Figtree
Genomics Multi-tool Websites
Gene ontology analysis
-DAVID - gene ontology analysis tool
-ReVigo - reduce & visualize gene ontology
-GoSlims - summarizing GO terems
RNAseq analysis
-Samtools
-BWA
-STEM - short time series expression miner
Pathway Analysis
Repeat Analysis
-RepeatModeler
-Repbase
-PALfinder
-Pclouds
Assembly
-SoapDeNovo
-SCUBAT (using RNAseq to improve scaffolding)
Genome Alignment
Genome Annotation
WHAT WE DO IN THE LAB
Evolutionary Genomics
Reptiles, esp. Snake Genomics
Genomics of Extreme Adaptations
Systems Biology
Population Genomics
LAB LINKS
Lab Research
Joining the Lab
