diff --git a/topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_Fasta.png b/topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_Fasta.png similarity index 100% rename from topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_Fasta.png rename to topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_Fasta.png diff --git a/topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_alleles.png b/topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_alleles.png similarity index 100% rename from topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_alleles.png rename to topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_alleles.png diff --git a/topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_models.png b/topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_models.png similarity index 100% rename from topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_models.png rename to topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_models.png diff --git a/topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_snps.png b/topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_snps.png similarity index 100% rename from topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_snps.png rename to topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_snps.png diff --git a/topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags.png b/topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags.png similarity index 100% rename from topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags.png rename to topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags.png diff --git a/topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags_SNP_visualization.png b/topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags_SNP_visualization.png similarity index 100% rename from topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags_SNP_visualization.png rename to topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags_SNP_visualization.png diff --git a/topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags_primary_secondary_reads.png b/topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags_primary_secondary_reads.png similarity index 100% rename from topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags_primary_secondary_reads.png rename to topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_female_tags_primary_secondary_reads.png diff --git a/topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_ustacks_in.png b/topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_ustacks_in.png similarity index 100% rename from topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_ustacks_in.png rename to topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_ustacks_in.png diff --git a/topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_ustacks_out.png b/topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_ustacks_out.png similarity index 100% rename from topics/sequence-analysis/images/RAD1_SNP_calling/RAD1_SNP_calling_ustacks_out.png rename to topics/ecology/images/RAD1_SNP_calling/RAD1_SNP_calling_ustacks_out.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/Genetic_map_CrossPollination.png b/topics/ecology/images/RAD2_Genetic_Map/Genetic_map_CrossPollination.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/Genetic_map_CrossPollination.png rename to topics/ecology/images/RAD2_Genetic_Map/Genetic_map_CrossPollination.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/Genetic_map_F2.png b/topics/ecology/images/RAD2_Genetic_Map/Genetic_map_F2.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/Genetic_map_F2.png rename to topics/ecology/images/RAD2_Genetic_Map/Genetic_map_F2.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/Genotypes_in.png b/topics/ecology/images/RAD2_Genetic_Map/Genotypes_in.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/Genotypes_in.png rename to topics/ecology/images/RAD2_Genetic_Map/Genotypes_in.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/Input_demultiplexed_files.png b/topics/ecology/images/RAD2_Genetic_Map/Input_demultiplexed_files.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/Input_demultiplexed_files.png rename to topics/ecology/images/RAD2_Genetic_Map/Input_demultiplexed_files.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_cstacks.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_cstacks.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_cstacks.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_cstacks.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_end.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_end.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_end.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_end.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_genotypes1.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_genotypes1.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_genotypes1.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_genotypes1.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_genotypes2.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_genotypes2.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_genotypes2.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_genotypes2.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_sstacks.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_sstacks.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_sstacks.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_sstacks.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_top.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_top.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_top.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_top.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_ustacks.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_ustacks.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_log_ustacks.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_log_ustacks.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches1.PNG b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches1.PNG similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches1.PNG rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches1.PNG diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches2.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches2.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches2.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches2.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches_alleles_haplotypes.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches_alleles_haplotypes.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches_alleles_haplotypes.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches_alleles_haplotypes.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches_alleles_male_female.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches_alleles_male_female.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches_alleles_male_female.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches_alleles_male_female.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches_markers.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches_markers.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches_markers.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches_markers.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches_snps.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches_snps.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches_snps.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches_snps.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches_snps_male_female.png b/topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches_snps_male_female.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovo_map_matches_snps_male_female.png rename to topics/ecology/images/RAD2_Genetic_Map/denovo_map_matches_snps_male_female.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovomap_in.png b/topics/ecology/images/RAD2_Genetic_Map/denovomap_in.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovomap_in.png rename to topics/ecology/images/RAD2_Genetic_Map/denovomap_in.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/denovomap_out.png b/topics/ecology/images/RAD2_Genetic_Map/denovomap_out.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/denovomap_out.png rename to topics/ecology/images/RAD2_Genetic_Map/denovomap_out.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/genotypes_automatic_correction.png b/topics/ecology/images/RAD2_Genetic_Map/genotypes_automatic_correction.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/genotypes_automatic_correction.png rename to topics/ecology/images/RAD2_Genetic_Map/genotypes_automatic_correction.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/genotypes_tsv.png b/topics/ecology/images/RAD2_Genetic_Map/genotypes_tsv.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/genotypes_tsv.png rename to topics/ecology/images/RAD2_Genetic_Map/genotypes_tsv.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/genotypes_txt.png b/topics/ecology/images/RAD2_Genetic_Map/genotypes_txt.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/genotypes_txt.png rename to topics/ecology/images/RAD2_Genetic_Map/genotypes_txt.png diff --git a/topics/sequence-analysis/images/RAD2_Genetic_Map/haplotypes_tsv.png b/topics/ecology/images/RAD2_Genetic_Map/haplotypes_tsv.png similarity index 100% rename from topics/sequence-analysis/images/RAD2_Genetic_Map/haplotypes_tsv.png rename to topics/ecology/images/RAD2_Genetic_Map/haplotypes_tsv.png diff --git a/topics/sequence-analysis/images/RAD3_Mini-contig/Input_data.png b/topics/ecology/images/RAD3_Mini-contig/Input_data.png similarity index 100% rename from topics/sequence-analysis/images/RAD3_Mini-contig/Input_data.png rename to topics/ecology/images/RAD3_Mini-contig/Input_data.png diff --git a/topics/sequence-analysis/images/RAD3_Mini-contig/assemblereadpairs.png b/topics/ecology/images/RAD3_Mini-contig/assemblereadpairs.png similarity index 100% rename from topics/sequence-analysis/images/RAD3_Mini-contig/assemblereadpairs.png rename to topics/ecology/images/RAD3_Mini-contig/assemblereadpairs.png diff --git a/topics/sequence-analysis/images/RAD3_Mini-contig/denovomap.png b/topics/ecology/images/RAD3_Mini-contig/denovomap.png similarity index 100% rename from topics/sequence-analysis/images/RAD3_Mini-contig/denovomap.png rename to topics/ecology/images/RAD3_Mini-contig/denovomap.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/Hohenlohe_et_al_2010.png b/topics/ecology/images/RAD4_Population_Genomics/Hohenlohe_et_al_2010.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/Hohenlohe_et_al_2010.png rename to topics/ecology/images/RAD4_Population_Genomics/Hohenlohe_et_al_2010.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/Input_data_ENA.png b/topics/ecology/images/RAD4_Population_Genomics/Input_data_ENA.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/Input_data_ENA.png rename to topics/ecology/images/RAD4_Population_Genomics/Input_data_ENA.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/Process_radtags_charts_end.PNG b/topics/ecology/images/RAD4_Population_Genomics/Process_radtags_charts_end.PNG similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/Process_radtags_charts_end.PNG rename to topics/ecology/images/RAD4_Population_Genomics/Process_radtags_charts_end.PNG diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/Process_radtags_charts_tablemodif_view.PNG b/topics/ecology/images/RAD4_Population_Genomics/Process_radtags_charts_tablemodif_view.PNG similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/Process_radtags_charts_tablemodif_view.PNG rename to topics/ecology/images/RAD4_Population_Genomics/Process_radtags_charts_tablemodif_view.PNG diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/Process_radtags_in.png b/topics/ecology/images/RAD4_Population_Genomics/Process_radtags_in.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/Process_radtags_in.png rename to topics/ecology/images/RAD4_Population_Genomics/Process_radtags_in.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/Process_radtags_out_parameter.png b/topics/ecology/images/RAD4_Population_Genomics/Process_radtags_out_parameter.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/Process_radtags_out_parameter.png rename to topics/ecology/images/RAD4_Population_Genomics/Process_radtags_out_parameter.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/Process_radtags_out_parameter2.png b/topics/ecology/images/RAD4_Population_Genomics/Process_radtags_out_parameter2.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/Process_radtags_out_parameter2.png rename to topics/ecology/images/RAD4_Population_Genomics/Process_radtags_out_parameter2.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/denovo_out.png b/topics/ecology/images/RAD4_Population_Genomics/denovo/denovo_out.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/denovo_out.png rename to topics/ecology/images/RAD4_Population_Genomics/denovo/denovo_out.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/output_X_fst_Y-Z_tsv_1.png b/topics/ecology/images/RAD4_Population_Genomics/denovo/output_X_fst_Y-Z_tsv_1.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/output_X_fst_Y-Z_tsv_1.png rename to topics/ecology/images/RAD4_Population_Genomics/denovo/output_X_fst_Y-Z_tsv_1.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/output_X_fst_Y-Z_tsv_2.png b/topics/ecology/images/RAD4_Population_Genomics/denovo/output_X_fst_Y-Z_tsv_2.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/output_X_fst_Y-Z_tsv_2.png rename to topics/ecology/images/RAD4_Population_Genomics/denovo/output_X_fst_Y-Z_tsv_2.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/output_sumstats_summary_tsv.png b/topics/ecology/images/RAD4_Population_Genomics/denovo/output_sumstats_summary_tsv.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/output_sumstats_summary_tsv.png rename to topics/ecology/images/RAD4_Population_Genomics/denovo/output_sumstats_summary_tsv.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/output_sumstats_tsv_1.png b/topics/ecology/images/RAD4_Population_Genomics/denovo/output_sumstats_tsv_1.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/output_sumstats_tsv_1.png rename to topics/ecology/images/RAD4_Population_Genomics/denovo/output_sumstats_tsv_1.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/output_sumstats_tsv_2.png b/topics/ecology/images/RAD4_Population_Genomics/denovo/output_sumstats_tsv_2.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/output_sumstats_tsv_2.png rename to topics/ecology/images/RAD4_Population_Genomics/denovo/output_sumstats_tsv_2.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/populations_in.png b/topics/ecology/images/RAD4_Population_Genomics/denovo/populations_in.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/populations_in.png rename to topics/ecology/images/RAD4_Population_Genomics/denovo/populations_in.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/populations_log.png b/topics/ecology/images/RAD4_Population_Genomics/denovo/populations_log.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/populations_log.png rename to topics/ecology/images/RAD4_Population_Genomics/denovo/populations_log.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/populations_out.png b/topics/ecology/images/RAD4_Population_Genomics/denovo/populations_out.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/denovo/populations_out.png rename to topics/ecology/images/RAD4_Population_Genomics/denovo/populations_out.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/multiqc.PNG b/topics/ecology/images/RAD4_Population_Genomics/multiqc.PNG similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/multiqc.PNG rename to topics/ecology/images/RAD4_Population_Genomics/multiqc.PNG diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/reference/Map_with_BWA.png b/topics/ecology/images/RAD4_Population_Genomics/reference/Map_with_BWA.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/reference/Map_with_BWA.png rename to topics/ecology/images/RAD4_Population_Genomics/reference/Map_with_BWA.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/reference/custom_build.png b/topics/ecology/images/RAD4_Population_Genomics/reference/custom_build.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/reference/custom_build.png rename to topics/ecology/images/RAD4_Population_Genomics/reference/custom_build.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/reference/custom_build_association.png b/topics/ecology/images/RAD4_Population_Genomics/reference/custom_build_association.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/reference/custom_build_association.png rename to topics/ecology/images/RAD4_Population_Genomics/reference/custom_build_association.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/reference/cut_columns_barcodes.png b/topics/ecology/images/RAD4_Population_Genomics/reference/cut_columns_barcodes.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/reference/cut_columns_barcodes.png rename to topics/ecology/images/RAD4_Population_Genomics/reference/cut_columns_barcodes.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/reference/populations_out.png b/topics/ecology/images/RAD4_Population_Genomics/reference/populations_out.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/reference/populations_out.png rename to topics/ecology/images/RAD4_Population_Genomics/reference/populations_out.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/reference/reference_map_in.png b/topics/ecology/images/RAD4_Population_Genomics/reference/reference_map_in.png similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/reference/reference_map_in.png rename to topics/ecology/images/RAD4_Population_Genomics/reference/reference_map_in.png diff --git a/topics/sequence-analysis/images/RAD4_Population_Genomics/reference/trackster_visualization.PNG b/topics/ecology/images/RAD4_Population_Genomics/reference/trackster_visualization.PNG similarity index 100% rename from topics/sequence-analysis/images/RAD4_Population_Genomics/reference/trackster_visualization.PNG rename to topics/ecology/images/RAD4_Population_Genomics/reference/trackster_visualization.PNG diff --git a/topics/sequence-analysis/images/denovo_based_workflow.PNG b/topics/ecology/images/denovo_based_workflow.PNG similarity index 100% rename from topics/sequence-analysis/images/denovo_based_workflow.PNG rename to topics/ecology/images/denovo_based_workflow.PNG diff --git a/topics/sequence-analysis/images/genetic_map_workflow.PNG b/topics/ecology/images/genetic_map_workflow.PNG similarity index 100% rename from topics/sequence-analysis/images/genetic_map_workflow.PNG rename to topics/ecology/images/genetic_map_workflow.PNG diff --git a/topics/sequence-analysis/images/ref_based_workflow.PNG b/topics/ecology/images/ref_based_workflow.PNG similarity index 100% rename from topics/sequence-analysis/images/ref_based_workflow.PNG rename to topics/ecology/images/ref_based_workflow.PNG diff --git a/topics/sequence-analysis/tutorials/de-novo-rad-seq/data-library.yaml b/topics/ecology/tutorials/de-novo-rad-seq/data-library.yaml similarity index 100% rename from topics/sequence-analysis/tutorials/de-novo-rad-seq/data-library.yaml rename to topics/ecology/tutorials/de-novo-rad-seq/data-library.yaml diff --git a/topics/sequence-analysis/tutorials/de-novo-rad-seq/tours/tour.yaml b/topics/ecology/tutorials/de-novo-rad-seq/tours/tour.yaml similarity index 100% rename from topics/sequence-analysis/tutorials/de-novo-rad-seq/tours/tour.yaml rename to topics/ecology/tutorials/de-novo-rad-seq/tours/tour.yaml diff --git a/topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial.md b/topics/ecology/tutorials/de-novo-rad-seq/tutorial.md similarity index 99% rename from topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial.md rename to topics/ecology/tutorials/de-novo-rad-seq/tutorial.md index 70b46938640c40..0a445a8d833f24 100644 --- a/topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial.md +++ b/topics/ecology/tutorials/de-novo-rad-seq/tutorial.md @@ -22,7 +22,7 @@ In the study of [Hohenlohe *et al.* 2010](http://journals.plos.org/plosgenetics/ ![Abstract of the paper on Population Genomics](../../images/RAD4_Population_Genomics/Hohenlohe_et_al_2010.png) -We here proposed to re-analyze these data at least until the population genomics statistics calculation step using STACKS pipeline. Existing *Gasterosteus aculeatus* draft genome will not be used here so the analysis will be performed de novo. In a de novo RAD-seq data analysis, the reads are aligned one on each other to create stacks and then clustered to build loci. A reference approach can also be conducted (see [ref_based tutorial]({{site.baseurl}}{% link topics/sequence-analysis/tutorials/ref-based-rad-seq/tutorial.md %}), allowing to work on existing assembled loci). +We here proposed to re-analyze these data at least until the population genomics statistics calculation step using STACKS pipeline. Existing *Gasterosteus aculeatus* draft genome will not be used here so the analysis will be performed de novo. In a de novo RAD-seq data analysis, the reads are aligned one on each other to create stacks and then clustered to build loci. A reference approach can also be conducted (see [ref_based tutorial]({{site.baseurl}}{% link topics/ecology/tutorials/ref-based-rad-seq/tutorial.md %}), allowing to work on existing assembled loci). > ### Agenda diff --git a/topics/sequence-analysis/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.ga b/topics/ecology/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.ga similarity index 100% rename from topics/sequence-analysis/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.ga rename to topics/ecology/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.ga diff --git a/topics/sequence-analysis/tutorials/genetic-map-rad-seq/data-library.yaml b/topics/ecology/tutorials/genetic-map-rad-seq/data-library.yaml similarity index 100% rename from topics/sequence-analysis/tutorials/genetic-map-rad-seq/data-library.yaml rename to topics/ecology/tutorials/genetic-map-rad-seq/data-library.yaml diff --git a/topics/sequence-analysis/tutorials/genetic-map-rad-seq/tours/tour.yaml b/topics/ecology/tutorials/genetic-map-rad-seq/tours/tour.yaml similarity index 100% rename from topics/sequence-analysis/tutorials/genetic-map-rad-seq/tours/tour.yaml rename to topics/ecology/tutorials/genetic-map-rad-seq/tours/tour.yaml diff --git a/topics/sequence-analysis/tutorials/genetic-map-rad-seq/tutorial.md b/topics/ecology/tutorials/genetic-map-rad-seq/tutorial.md similarity index 100% rename from topics/sequence-analysis/tutorials/genetic-map-rad-seq/tutorial.md rename to topics/ecology/tutorials/genetic-map-rad-seq/tutorial.md diff --git a/topics/sequence-analysis/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.ga b/topics/ecology/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.ga similarity index 100% rename from topics/sequence-analysis/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.ga rename to topics/ecology/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.ga diff --git a/topics/sequence-analysis/tutorials/ref-based-rad-seq/data-library.yaml b/topics/ecology/tutorials/ref-based-rad-seq/data-library.yaml similarity index 100% rename from topics/sequence-analysis/tutorials/ref-based-rad-seq/data-library.yaml rename to topics/ecology/tutorials/ref-based-rad-seq/data-library.yaml diff --git a/topics/sequence-analysis/tutorials/ref-based-rad-seq/tours/tour.yaml b/topics/ecology/tutorials/ref-based-rad-seq/tours/tour.yaml similarity index 100% rename from topics/sequence-analysis/tutorials/ref-based-rad-seq/tours/tour.yaml rename to topics/ecology/tutorials/ref-based-rad-seq/tours/tour.yaml diff --git a/topics/sequence-analysis/tutorials/ref-based-rad-seq/tutorial.md b/topics/ecology/tutorials/ref-based-rad-seq/tutorial.md similarity index 100% rename from topics/sequence-analysis/tutorials/ref-based-rad-seq/tutorial.md rename to topics/ecology/tutorials/ref-based-rad-seq/tutorial.md diff --git a/topics/sequence-analysis/tutorials/ref-based-rad-seq/workflows/Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.ga b/topics/ecology/tutorials/ref-based-rad-seq/workflows/Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.ga similarity index 100% rename from topics/sequence-analysis/tutorials/ref-based-rad-seq/workflows/Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.ga rename to topics/ecology/tutorials/ref-based-rad-seq/workflows/Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.ga diff --git a/topics/sequence-analysis/tutorials/ref-based-rad-seq/workflows/workflow.ga b/topics/ecology/tutorials/ref-based-rad-seq/workflows/workflow.ga similarity index 100% rename from topics/sequence-analysis/tutorials/ref-based-rad-seq/workflows/workflow.ga rename to topics/ecology/tutorials/ref-based-rad-seq/workflows/workflow.ga diff --git a/topics/sequence-analysis/images/Stacks_M_parameter_within_ind_dist.png b/topics/sequence-analysis/images/Stacks_M_parameter_within_ind_dist.png deleted file mode 100644 index 2392f72c879291..00000000000000 Binary files a/topics/sequence-analysis/images/Stacks_M_parameter_within_ind_dist.png and /dev/null differ diff --git a/topics/sequence-analysis/images/Stacks_components.png b/topics/sequence-analysis/images/Stacks_components.png deleted file mode 100644 index 4dcf54a69ebef0..00000000000000 Binary files a/topics/sequence-analysis/images/Stacks_components.png and /dev/null differ diff --git a/topics/sequence-analysis/images/Stacks_m_parameter_stack_depth.png b/topics/sequence-analysis/images/Stacks_m_parameter_stack_depth.png deleted file mode 100644 index a6c8d2922daddf..00000000000000 Binary files a/topics/sequence-analysis/images/Stacks_m_parameter_stack_depth.png and /dev/null differ diff --git a/topics/sequence-analysis/images/Stacks_pipelines.png b/topics/sequence-analysis/images/Stacks_pipelines.png deleted file mode 100644 index 429a9752d59ee9..00000000000000 Binary files a/topics/sequence-analysis/images/Stacks_pipelines.png and /dev/null differ