https://darencard.github.io/blog/2014-02-04-python-genome-published/ 2014-02-04T00:00:00+00:00 https://darencard.github.io/blog/2014-02-10-rosalind-bioinformatics/ 2014-02-10T00:00:00+00:00 https://darencard.github.io/blog/2014-02-11-ncbi-sra-submission/ 2014-02-11T00:00:00+00:00 https://darencard.github.io/blog/2014-03-24-batch-ensembl-download/ 2014-03-24T00:00:00+00:00 https://darencard.github.io/blog/2015-08-19-genotype-matrix-creation/ 2015-08-19T00:00:00+00:00 https://darencard.github.io/blog/2015-10-06-sra-batch-download/ 2015-10-06T00:00:00+00:00 https://darencard.github.io/blog/2015-10-07-reference-guided-assembly-best-practices/ 2015-10-07T00:00:00+00:00 https://darencard.github.io/blog/2017-01-13-missing-data-proportions-vcf/ 2017-01-13T00:00:00+00:00 https://darencard.github.io/blog/2017-03-03-efficient-repeatmodeler/ 2017-03-03T00:00:00+00:00 https://darencard.github.io/blog/2017-03-03-imagej-macros-scale-png/ 2017-03-03T00:00:00+00:00 https://darencard.github.io/blog/2017-03-04-image-dimensions/ 2017-03-04T00:00:00+00:00 https://darencard.github.io/blog/2017-04-11-genomics-oneliners/ 2017-04-11T00:00:00+00:00 https://darencard.github.io/blog/2017-05-02-auto-git-file/ 2017-05-02T00:00:00+00:00 https://darencard.github.io/blog/2017-05-16-maker-genome-annotation/ 2017-05-16T00:00:00+00:00 https://darencard.github.io/blog/2017-07-02-configuring-jbrowse/ 2017-07-02T00:00:00+00:00 https://darencard.github.io/blog/2017-07-12-plotly-tutorial/ 2017-07-12T00:00:00+00:00 https://darencard.github.io/blog/2017-07-18-oneliners-popstats-from-vcf/ 2017-07-18T00:00:00+00:00 https://darencard.github.io/blog/2017-08-02-gdrive-download-bash/ 2017-08-02T00:00:00+00:00 https://darencard.github.io/blog/2017-08-26-SLiM-intro-annotation-simulation/ 2017-08-26T00:00:00+00:00 https://darencard.github.io/blog/2017-08-31-gnuplot-quickstart/ 2017-08-31T00:00:00+00:00 https://darencard.github.io/blog/2018-01-10-gene-structure-summary/ 2018-01-10T00:00:00+00:00 https://darencard.github.io/blog/2018-01-10-variant-effect-analysis/ 2018-01-10T00:00:00+00:00 https://darencard.github.io/blog/2018-01-12-orthomcl-tutorial/ 2018-01-12T00:00:00+00:00 https://darencard.github.io/blog/2018-01-18-spliced-sequence-extract-gff/ 2018-01-18T00:00:00+00:00 https://darencard.github.io/blog/2018-01-29-scrolling-DNA-colored/ 2018-01-29T00:00:00+00:00 https://darencard.github.io/blog/2018-05-15-prfb-award-announcement/ 2018-05-15T00:00:00+00:00 https://darencard.github.io/blog/2018-07-19-dissertation-defense/ 2018-07-19T00:00:00+00:00 https://darencard.github.io/blog/2018-08-14-entware-synology/ 2018-08-14T00:00:00+00:00 https://darencard.github.io/blog/2017-09-07-extract-fastq-bam/ 2018-09-07T00:00:00+00:00 https://darencard.github.io/blog/2018-09-30-python-adaptation-pub/ 2018-09-30T00:00:00+00:00 https://darencard.github.io/blog/2018-10-04-basespace-quickstart/ 2018-10-04T00:00:00+00:00 https://darencard.github.io/blog/2018-10-11-install-run-provean-notes/ 2018-10-11T00:00:00+00:00 https://darencard.github.io/blog/2018-10-11-phastcons-conserved-region-extraction/ 2018-10-11T00:00:00+00:00 https://darencard.github.io/blog/2018-10-24-australia-arrival/ 2018-10-24T00:00:00+00:00 https://darencard.github.io/blog/2019-01-25-UCSC-genome-track-setup/ 2019-01-25T00:00:00+00:00 https://darencard.github.io/blog/2019-01-25-markdown-embedding-gists/ 2019-01-25T00:00:00+00:00 https://darencard.github.io/blog/2019-02-15-australia-recap/ 2019-02-15T00:00:00+00:00 https://darencard.github.io/blog/2019-03-25-rattlesnake-genome-published/ 2019-03-25T00:00:00+00:00 https://darencard.github.io/blog/2019-09-03-vgp-ebp-meeting/ 2019-09-03T00:00:00+00:00 https://darencard.github.io/blog/2019-09-13-determining-stranded-rnaseq/ 2019-09-13T00:00:00+00:00 https://darencard.github.io/blog/2019-09-15-radseq-intro-lesson/ 2019-09-15T00:00:00+00:00 https://darencard.github.io/blog/2019-09-19-zotero-file-relink/ 2019-09-19T00:00:00+00:00 https://darencard.github.io/blog/2019-09-27-remove-box-space/ 2019-09-27T00:00:00+00:00 https://darencard.github.io/blog/2019-10-22-msprime-tutorial/ 2019-10-22T00:00:00+00:00 https://darencard.github.io/blog/2019-10-22-odyssey-cpan-config/ 2019-10-26T00:00:00+00:00 https://darencard.github.io/blog/2019-11-01-whole-genome-alignment-tutorial/ 2019-11-01T00:00:00+00:00 https://darencard.github.io/blog/2019-12-20-RAD-locus-footprints/ 2019-12-26T00:00:00+00:00 https://darencard.github.io/blog/2020-07-23-augustus-optimization/ 2020-07-23T00:00:00+00:00 https://darencard.github.io/blog/2022-06-09-downwards-axis-text-ggplot2/ 2022-06-08T00:00:00+00:00 https://darencard.github.io/blog/2022-07-09-genome-repeat-annotation/ 2022-07-09T00:00:00+00:00 https://darencard.github.io/blog/2022-07-16-genomics-data-management/ 2022-07-16T00:00:00+00:00 https://darencard.github.io/blog/2022-07-29-purge-phylogenetic-redundancy/ 2022-07-29T00:00:00+00:00 https://darencard.github.io/blog/2022-10-13-install-repeat-modeler-masker/ 2022-10-13T00:00:00+00:00 https://darencard.github.io/blog/2022-10-22-bonferonni-benjamini-hochberg-large-dataset/ 2022-10-22T00:00:00+00:00 https://darencard.github.io/blog/2024-03-13-preparing-archiving-resurrecting-data-harvard-tape/ 2024-03-13T00:00:00+00:00 https://darencard.github.io/events/2016-04-02-uta-swc-python/ 2016-04-02T00:00:00+00:00 https://darencard.github.io/events/2016-10-15-uta-swc-r/ 2016-10-15T00:00:00+00:00 https://darencard.github.io/events/2017-02-04-uta-swc-python/ 2017-02-04T00:00:00+00:00 https://darencard.github.io/events/2017-11-11-uta-swc-r/ 2017-11-11T00:00:00+00:00 https://darencard.github.io/events/2018-02-24-uta-swc-python/ 2018-02-24T00:00:00+00:00 https://darencard.github.io/events/2018-09-22-uta-swc-r/ 2018-09-22T00:00:00+00:00 https://darencard.github.io/templates/YYYY-MM-DD-blog-post-template/ https://darencard.github.io/templates/YYYY-MM-DD-event-template/ https://darencard.github.io/templates/YYYY-MM-DD-meeting-minutes-template/ https://darencard.github.io/blog/ https://darencard.github.io/diversity/ https://darencard.github.io/evol2021/ https://darencard.github.io/ https://darencard.github.io/links/ https://darencard.github.io/outreach/ https://darencard.github.io/publications/ https://darencard.github.io/research/ https://darencard.github.io/teaching/ https://darencard.github.io/publications/ https://darencard.github.io/assets/scripts/ https://darencard.github.io/assets/pdfs/AdamsRA_2016_Genome_Microsatellite_landscape_evolutionary_dynamics_across_450_million_years_of_vertebrate_genome_evolution.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/AdamsRA_2017_Bioinformatics_GppFst_-_genomic_posterior_predictive_simulations_of_FST_and_dXY_for_identifying_outlier_loci_from_population_genomic_data.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/AdamsRA_2018_Bioinformatics_ThetaMater_-_Bayesian_estimation_of_population_size_parameter_%CE%B8_from_genomic_data.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/AdamsRA_2018_Syst_Biol_Assessing_the_Impacts_of_Positive_Selection_on_Coalescent-Based_Species_Tree_Estimation_and_Species_Delimitation.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/AndrewAA_2015_Physiological_Genomics_Rapid_changes_in_gene_expression_direct_rapid_shifts_in_intestinal_form_and_function_in_the_Burmese_python_after_feeding.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/AndrewAA_2017_BMC_Genomics_Growth_and_stress_response_mechanisms_underlying_post-feeding_regenerative_organ_growth_in_the_Burmese_python.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CardDC_2014_PLOS_ONE_Two_Low_Coverage_Bird_Genomes_and_a_Comparison_of_Reference-Guided_versus_De_Novo_Genome_Assemblies.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CardDC_2016_Molecular_Phylogenetics_and_Evolution_Phylogeographic_and_population_genetic_analyses_reveal_multiple_species_of_Boa_and_independent_origins_of_insular_dwarfism.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CardDC_2018_Molecular_Ecology_Novel_ecological_and_climatic_conditions_drive_rapid_adaptation_in_invasive_Florida_Burmese_pythons.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CardDC_2018_Molecular_Ecology_Plasticity_and_local_adaptation_explain_lizard_cold_tolerance.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CardDC_2019_Genome_Biol_Evol_Genomic_Basis_of_Convergent_Island_Phenotypes_in_Boa_Constrictors.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CardDC_2021_Genome-wide_data_implicate_terminal_fusion_automixis_in_king_cobra_facultative.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CardDC_2021_Museum_genomics.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CardDC_2022_Structure_and_evolution_of_the_squamate_major_histocompatibility_complex_as.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CardDC_2023_Genome_Evolution_and_the_Future_of_Phylogenomics_of_Non-Avian_Reptiles.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CasewellNC_2019_PNAS_Solenodon_genome_reveals_convergent_evolution_of_venom_in_eulipotyphlan_mammals.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CasewellNC_2019_PNAS_Solenodon_genome_reveals_convergent_evolution_of_venom_in_eulipotyphlan_mammals2.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CastoeTC_2013_PNAS_The_Burmese_python_genome_reveals_the_molecular_basis_for_extreme_adaptation_in_snakes.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/CoxRC_2017_The_American_Naturalist_Hormonally_Mediated_Increases_in_Sex-Biased_Gene_Expression_Accompany_the_Breakdown_of_Between-Sex_Genetic_Correlations_in_a_Sexually_Dimorphic_Lizard.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/FarleighKF_2021_The_effects_of_climate_and_demographic_history_in_shaping_genomic_variation.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/GambleTG_2017_Current_Biology_The_Discovery_of_XY_Sex_Chromosomes_in_a_Boa_and_Python.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/GilbertCG_2014_Proceedings_of_the_Royal_Society_of_London_B_Biological_Sciences_Endogenous_hepadnaviruses,_bornaviruses_and_circoviruses_in_snakes.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/HalesNH_2017_Mol_Ecol_Contrasting_gene_expression_programs_correspond_with_predator-induced_phenotypic_plasticity_within_and_across_generations_in_Daphnia.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/JezkovaTJ_2015_Molecular_Ecology_Genetic_consequences_of_postglacial_range_expansion_in_two_codistributed_rodents_(genus_Dipodomys)_depend_on_ecology_and_genetic_locus.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/KaziMK_J_Antimicrob_Chemother_Discovery_and_characterization_of_New_Delhi_metallo-%CE%B2-lactamase-1_inhibitor.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/KoochekianNK_2022_GigaScience_A_chromosome-level_genome_assembly_and_annotation_of_the_desert_horned_lizard,.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/LamichhaneySL_2019_Philosophical_Transactions_of_the_Royal_Society_B_Biological_Sciences_Integrating_natural_history_collections_and_comparative_genomics_to_study_the_genetic_architecture_of_convergent_evolution.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/LotterhosKL_2017_Methods_Ecol_Evol_Composite_measures_of_selection_can_improve_the_signal-to-noise_ratio_in_genome_scans.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/PasquesiGP_2018_Nature_Communications_Squamate_reptiles_challenge_paradigms_of_genomic_repeat_element_evolution_set_by_birds_and_mammals.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/PerryBP_2018_Genome_Biol_Evol_Molecular_Adaptations_for_Sensing_and_Securing_Prey_and_Insight_into_Amniote_Genome_Diversity_from_the_Garter_Snake_Genome.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/PerryBP_2019_Proceedings_of_the_Royal_Society_B_Biological_Sciences_Multi-species_comparisons_of_snakes_identify_coordinated_signalling_networks_underlying_post-feeding_intestinal_regeneration.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/PintoBP_2019_Developmental_Dynamics_The_transcriptome_of_the_veiled_chameleon_(Chamaeleo_calyptratus)_-_A_resource_for_studying_the_evolution_and_development_of_vertebrates.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/Reyes-VelascoJR_2015_Mol_Biol_Evol_Expression_of_Venom_Gene_Homologs_in_Diverse_Python_Tissues_Suggests_a_New_Model_for_the_Evolution_of_Snake_Venom.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/SchieldDS_2015_Molecular_Phylogenetics_and_Evolution_Incipient_speciation_with_biased_gene_flow_between_two_lineages_of_the_Western_Diamondback_Rattlesnake_(Crotalus_atrox).pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/SchieldDS_2016_Methods_Ecol_Evol_EpiRADseq_-_scalable_analysis_of_genomewide_patterns_of_methylation_using_next-generation_sequencing.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/SchieldDS_2017_Ecol_Evol_Insight_into_the_roles_of_selection_in_speciation_from_genomic_patterns_of_divergence_and_introgression_in_secondary_contact_in_venomous_rattlesnakes.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/SchieldDS_2018_Molecular_Phylogenetics_and_Evolution_Cryptic_genetic_diversity,_population_structure,_and_gene_flow_in_the_Mojave_rattlesnake_(Crotalus_scutulatus).pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/SchieldDS_2019_Biol_J_Linn_Soc_Allopatric_divergence_and_secondary_contact_with_gene_flow_-_a_recurring_theme.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/SchieldDS_2019_Genome_Res._The_origins_and_evolution_of_chromosomes,_dosage_compensation,_and_mechanisms_underlying_venom_regulation_in_snakes.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/SchieldDS_2022_Genome_Biology_and_Evolution_The_Rattlesnake_W_Chromosome.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/SchottRS_2017_Genome_Biol_Evol_Targeted_Capture_of_Complete_Coding_Regions_across_Divergent_Species.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/SchottRS_2018_Mol_Biol_Evol_Shifts_in_Selective_Pressures_on_Snake_Phototransduction_Genes_Associated_with_Photoreceptor_Transmutation_and_Dim-Light_Ancestry.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/ShaneyKS_2014_Toxinology_Squamate_Reptile_Genomics_and_Evolution.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/ShorttJS_2017_PLOS_Neglected_Tropical_Diseases_Whole_Genome_Amplification_and_Reduced-Representation_Genome_Sequencing_of_Schistosoma_japonicum_Miracidia.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/StreicherJS_2016_Evolution_Genetic_surfing,_not_allopatric_divergence,_explains_spatial_sorting_of_mitochondrial_haplotypes_in_venomous_coralsnakes.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/assets/pdfs/VerityRV_2017_Mol_Ecol_Resour_minotaur_-_A_platform_for_the_analysis_and_visualization_of_multivariate_results_from_genome_scans_with_R_Shiny.pdf 2025-05-12T14:50:10+00:00 https://darencard.github.io/files/RADseq_introduction.pdf 2025-05-12T14:50:10+00:00