├── AdjustFASTA_or_FASTQ ├── README.md ├── add_source_organism_info_to_FASTA.py ├── delete_seq_following_pattern_within_FASTA.py ├── demo delete_seq_following_pattern_within_multiFASTA.ipynb ├── demo permute_seq_within_FASTA_an_amount.ipynb ├── permute_seq_within_FASTA_an_amount.py ├── remove_seq_from_multiFASTA_with_match_in_description.py └── replace_unusual_nts_within_FASTA.py ├── Adjust_Annotation ├── README.md ├── fix_lsu_rRNA_annotation_in_gff_resulting_from_mfannot.py └── makes_length_annotation_file.py ├── Adjust_lists ├── README.md ├── cufflinksIDs_list_to_systematic_names.py ├── systematic_names_to_standard_names_using_cufflinks_gtf.py └── tx2gene_generator.py ├── CompareFASTA_or_FASTQ ├── README.md └── compare_organisms_in_two_files_of_fasta_entries.py ├── Compare_biological_seq_strings ├── README.md ├── report_diff_between_two_seq_strings.py └── stub of demo for report_diff_between_two_seq_strings script.ipynb ├── ConvertSeq ├── ConvertFASTAdnaSEQtoRNA.py ├── README.md ├── collapse_large_unknown_blocks_in_DNA_sequence.py └── convert_fasta_to_reverse_complement.py ├── CountFastaFastq ├── README.md └── count_fastq_entries.py ├── Extract_Conserved_from_Aligned ├── README.md └── extract_conserved_from_alignments.py ├── Extract_Details_or_Annotation ├── README.md ├── demo report_coordinates_for_seq_within_FASTA.ipynb ├── mine_SUTs_and_merge_into_mito_transcripts_df.py ├── mine_XUTs_and_merge_into_mito_transcripts_df.py ├── mine_mito_features_from_transcriptome.py ├── report_coordinates_for_seq_within_FASTA.py └── summarize_all_nts_even_ambiguous_present_in_FASTA.py ├── Extract_from_FASTA ├── README.md ├── demo get_seq_following_seq_from_FASTA.ipynb ├── extract_subsequence_from_FASTA.py ├── get_seq_following_seq_from_FASTA.py ├── get_seq_from_multiFASTA_with_match_in_description.py └── get_specified_length_of_end_of_seq_from_FASTA.py ├── FindSequence ├── README.md ├── demo find_sequence_element_occurrences_in_sequence script.ipynb └── find_sequence_element_occurrences_in_sequence.py ├── LookUpTaxon ├── LookUpTaxonFA.py ├── LookUpTaxonFAComD.py └── README.md ├── README.md ├── RetrieveSeq ├── GetmRNAforProtein.py ├── GetmRNAorCDSforProtein.py └── README.md ├── SOLiD ├── README.md ├── split_SOLiD_reads.py └── split_SOLiD_reads_basic.py ├── alignment-utilities ├── MSA_to_corresponding_residue_numbers.py ├── README.md ├── add_actual_position_numbering_to_sequence_in_top_line_of_clustal_output.py ├── calculate_cons_for_clustal_nucleic.py ├── calculate_cons_for_clustal_protein.py ├── categorize_residues_based_on_conservation_relative_consensus_line.py ├── check_seq_frag_in_MSAclustal_intact_viaFASTA.py ├── check_seq_in_MSAclustal_consistent_with_FASTA.py ├── demo roughly_score_relationships_to_subject_seq_pairwise_premsa.ipynb ├── extract_regions_from_clustal_alignment.py ├── mview_to_CLUSTAL.py ├── reverse_complement_of_clustal_alignment.py ├── roughly_score_relationships_to_subject_seq_pairwise_premsa.py ├── score_columns_in_clustal_msa.py ├── score_differences_between_sequences_by_pairwise_alignment.py ├── score_sequences_in_clustal_msa.py └── score_sequences_in_clustal_msa_favoring_top_line.py ├── annotation-utilities ├── README.md └── measure_intergenic_regions_in_mito_annotations.py ├── assess_coding_potential_and_changes └── README.md ├── bendit_server-utilities ├── README.md └── bendit_server_results_to_df.py ├── bendit_standalone-utilities ├── README.md └── bendit_standalone_results_to_df.py ├── blast-utilities ├── README.md ├── blast_to_df.py └── demo_blast2df_in_python2.ipynb ├── circos-utilities ├── README.md ├── UCSC_chrom_sizes_2_circos_karyotype.py └── demo UCSC_chrom_sizes_2_circos_karyotype script.ipynb ├── count_triplets ├── README.md └── triplet_frequency.py ├── ena-utilities └── README.md ├── hhsuite3-utilities ├── README.md ├── core_reduction_dataframe_steps_for_ECIIIL_genome.py ├── hhsuite3_results_to_df.py └── make_report_on_equivalents_of_interacting_residues.py ├── mcscan-utilities ├── README.md └── get_if_chromosome_rearranged_func_AFTER_MCscan_simplified.py ├── omega-presence ├── README.md ├── check_for_omega_HEG.py ├── check_for_omega_intron.py └── find_mito_fungal_lsu_rRNA_and_check_for_omega_intron.py ├── patmatch-utilities ├── README.md ├── matches_a_patmatch_pattern.py └── patmatch_results_to_df.py ├── plot_expression_across_chromosomes ├── LICENSE ├── README.md ├── example_imgs │ ├── genes_mean_TPM_across_chr.png │ ├── genes_mean_TPM_across_chr_IV_VIII_XII.png │ ├── genes_mean_TPM_across_chr_smooth.png │ ├── genes_mean_TPM_across_chrlines.png │ ├── genes_mean_TPM_across_chrnolog.png │ └── real_data_no_anueploidy.png ├── plot_expression_across_chromosomes.py └── plot_expression_across_chromosomes_direct.py ├── plot_nt_imbalance ├── README.md ├── imblance_plot_exmple.png ├── nucleotide_difference_imbalance_plot_stylized_like_Figure_8_of_Morrill_et_al_2016.py └── two_nucleotides_in_proximity_difference_imbalance_plot.py ├── plot_read_data ├── README.md ├── plot_5prime_end_from_bedgraph.py ├── plot_coverage.py └── plot_coverage_and_starts.py └── plot_sites ├── README.md ├── plot_sites_example_plot.png └── plot_sites_position_across_chromosome.py /AdjustFASTA_or_FASTQ/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/AdjustFASTA_or_FASTQ/README.md -------------------------------------------------------------------------------- /AdjustFASTA_or_FASTQ/add_source_organism_info_to_FASTA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/AdjustFASTA_or_FASTQ/add_source_organism_info_to_FASTA.py -------------------------------------------------------------------------------- /AdjustFASTA_or_FASTQ/delete_seq_following_pattern_within_FASTA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/AdjustFASTA_or_FASTQ/delete_seq_following_pattern_within_FASTA.py -------------------------------------------------------------------------------- /AdjustFASTA_or_FASTQ/demo delete_seq_following_pattern_within_multiFASTA.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/AdjustFASTA_or_FASTQ/demo delete_seq_following_pattern_within_multiFASTA.ipynb -------------------------------------------------------------------------------- /AdjustFASTA_or_FASTQ/demo permute_seq_within_FASTA_an_amount.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/AdjustFASTA_or_FASTQ/demo permute_seq_within_FASTA_an_amount.ipynb -------------------------------------------------------------------------------- /AdjustFASTA_or_FASTQ/permute_seq_within_FASTA_an_amount.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/AdjustFASTA_or_FASTQ/permute_seq_within_FASTA_an_amount.py -------------------------------------------------------------------------------- /AdjustFASTA_or_FASTQ/remove_seq_from_multiFASTA_with_match_in_description.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/AdjustFASTA_or_FASTQ/remove_seq_from_multiFASTA_with_match_in_description.py -------------------------------------------------------------------------------- /AdjustFASTA_or_FASTQ/replace_unusual_nts_within_FASTA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/AdjustFASTA_or_FASTQ/replace_unusual_nts_within_FASTA.py -------------------------------------------------------------------------------- /Adjust_Annotation/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Adjust_Annotation/README.md -------------------------------------------------------------------------------- /Adjust_Annotation/fix_lsu_rRNA_annotation_in_gff_resulting_from_mfannot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Adjust_Annotation/fix_lsu_rRNA_annotation_in_gff_resulting_from_mfannot.py -------------------------------------------------------------------------------- /Adjust_Annotation/makes_length_annotation_file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Adjust_Annotation/makes_length_annotation_file.py -------------------------------------------------------------------------------- /Adjust_lists/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Adjust_lists/README.md -------------------------------------------------------------------------------- /Adjust_lists/cufflinksIDs_list_to_systematic_names.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Adjust_lists/cufflinksIDs_list_to_systematic_names.py -------------------------------------------------------------------------------- /Adjust_lists/systematic_names_to_standard_names_using_cufflinks_gtf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Adjust_lists/systematic_names_to_standard_names_using_cufflinks_gtf.py -------------------------------------------------------------------------------- /Adjust_lists/tx2gene_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Adjust_lists/tx2gene_generator.py -------------------------------------------------------------------------------- /CompareFASTA_or_FASTQ/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/CompareFASTA_or_FASTQ/README.md -------------------------------------------------------------------------------- /CompareFASTA_or_FASTQ/compare_organisms_in_two_files_of_fasta_entries.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/CompareFASTA_or_FASTQ/compare_organisms_in_two_files_of_fasta_entries.py -------------------------------------------------------------------------------- /Compare_biological_seq_strings/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Compare_biological_seq_strings/README.md -------------------------------------------------------------------------------- /Compare_biological_seq_strings/report_diff_between_two_seq_strings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Compare_biological_seq_strings/report_diff_between_two_seq_strings.py -------------------------------------------------------------------------------- /Compare_biological_seq_strings/stub of demo for report_diff_between_two_seq_strings script.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Compare_biological_seq_strings/stub of demo for report_diff_between_two_seq_strings script.ipynb -------------------------------------------------------------------------------- /ConvertSeq/ConvertFASTAdnaSEQtoRNA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/ConvertSeq/ConvertFASTAdnaSEQtoRNA.py -------------------------------------------------------------------------------- /ConvertSeq/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/ConvertSeq/README.md -------------------------------------------------------------------------------- /ConvertSeq/collapse_large_unknown_blocks_in_DNA_sequence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/ConvertSeq/collapse_large_unknown_blocks_in_DNA_sequence.py -------------------------------------------------------------------------------- /ConvertSeq/convert_fasta_to_reverse_complement.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/ConvertSeq/convert_fasta_to_reverse_complement.py -------------------------------------------------------------------------------- /CountFastaFastq/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/CountFastaFastq/README.md -------------------------------------------------------------------------------- /CountFastaFastq/count_fastq_entries.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/CountFastaFastq/count_fastq_entries.py -------------------------------------------------------------------------------- /Extract_Conserved_from_Aligned/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_Conserved_from_Aligned/README.md -------------------------------------------------------------------------------- /Extract_Conserved_from_Aligned/extract_conserved_from_alignments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_Conserved_from_Aligned/extract_conserved_from_alignments.py -------------------------------------------------------------------------------- /Extract_Details_or_Annotation/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_Details_or_Annotation/README.md -------------------------------------------------------------------------------- /Extract_Details_or_Annotation/demo report_coordinates_for_seq_within_FASTA.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_Details_or_Annotation/demo report_coordinates_for_seq_within_FASTA.ipynb -------------------------------------------------------------------------------- /Extract_Details_or_Annotation/mine_SUTs_and_merge_into_mito_transcripts_df.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_Details_or_Annotation/mine_SUTs_and_merge_into_mito_transcripts_df.py -------------------------------------------------------------------------------- /Extract_Details_or_Annotation/mine_XUTs_and_merge_into_mito_transcripts_df.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_Details_or_Annotation/mine_XUTs_and_merge_into_mito_transcripts_df.py -------------------------------------------------------------------------------- /Extract_Details_or_Annotation/mine_mito_features_from_transcriptome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_Details_or_Annotation/mine_mito_features_from_transcriptome.py -------------------------------------------------------------------------------- /Extract_Details_or_Annotation/report_coordinates_for_seq_within_FASTA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_Details_or_Annotation/report_coordinates_for_seq_within_FASTA.py -------------------------------------------------------------------------------- /Extract_Details_or_Annotation/summarize_all_nts_even_ambiguous_present_in_FASTA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_Details_or_Annotation/summarize_all_nts_even_ambiguous_present_in_FASTA.py -------------------------------------------------------------------------------- /Extract_from_FASTA/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_from_FASTA/README.md -------------------------------------------------------------------------------- /Extract_from_FASTA/demo get_seq_following_seq_from_FASTA.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_from_FASTA/demo get_seq_following_seq_from_FASTA.ipynb -------------------------------------------------------------------------------- /Extract_from_FASTA/extract_subsequence_from_FASTA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_from_FASTA/extract_subsequence_from_FASTA.py -------------------------------------------------------------------------------- /Extract_from_FASTA/get_seq_following_seq_from_FASTA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_from_FASTA/get_seq_following_seq_from_FASTA.py -------------------------------------------------------------------------------- /Extract_from_FASTA/get_seq_from_multiFASTA_with_match_in_description.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_from_FASTA/get_seq_from_multiFASTA_with_match_in_description.py -------------------------------------------------------------------------------- /Extract_from_FASTA/get_specified_length_of_end_of_seq_from_FASTA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/Extract_from_FASTA/get_specified_length_of_end_of_seq_from_FASTA.py -------------------------------------------------------------------------------- /FindSequence/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/FindSequence/README.md -------------------------------------------------------------------------------- /FindSequence/demo find_sequence_element_occurrences_in_sequence script.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/FindSequence/demo find_sequence_element_occurrences_in_sequence script.ipynb -------------------------------------------------------------------------------- /FindSequence/find_sequence_element_occurrences_in_sequence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/FindSequence/find_sequence_element_occurrences_in_sequence.py -------------------------------------------------------------------------------- /LookUpTaxon/LookUpTaxonFA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/LookUpTaxon/LookUpTaxonFA.py -------------------------------------------------------------------------------- /LookUpTaxon/LookUpTaxonFAComD.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/LookUpTaxon/LookUpTaxonFAComD.py -------------------------------------------------------------------------------- /LookUpTaxon/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/LookUpTaxon/README.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/README.md -------------------------------------------------------------------------------- /RetrieveSeq/GetmRNAforProtein.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/RetrieveSeq/GetmRNAforProtein.py -------------------------------------------------------------------------------- /RetrieveSeq/GetmRNAorCDSforProtein.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/RetrieveSeq/GetmRNAorCDSforProtein.py -------------------------------------------------------------------------------- /RetrieveSeq/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/RetrieveSeq/README.md -------------------------------------------------------------------------------- /SOLiD/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/SOLiD/README.md -------------------------------------------------------------------------------- /SOLiD/split_SOLiD_reads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/SOLiD/split_SOLiD_reads.py -------------------------------------------------------------------------------- /SOLiD/split_SOLiD_reads_basic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/SOLiD/split_SOLiD_reads_basic.py -------------------------------------------------------------------------------- /alignment-utilities/MSA_to_corresponding_residue_numbers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/MSA_to_corresponding_residue_numbers.py -------------------------------------------------------------------------------- /alignment-utilities/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/README.md -------------------------------------------------------------------------------- /alignment-utilities/add_actual_position_numbering_to_sequence_in_top_line_of_clustal_output.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/add_actual_position_numbering_to_sequence_in_top_line_of_clustal_output.py -------------------------------------------------------------------------------- /alignment-utilities/calculate_cons_for_clustal_nucleic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/calculate_cons_for_clustal_nucleic.py -------------------------------------------------------------------------------- /alignment-utilities/calculate_cons_for_clustal_protein.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/calculate_cons_for_clustal_protein.py -------------------------------------------------------------------------------- /alignment-utilities/categorize_residues_based_on_conservation_relative_consensus_line.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/categorize_residues_based_on_conservation_relative_consensus_line.py -------------------------------------------------------------------------------- /alignment-utilities/check_seq_frag_in_MSAclustal_intact_viaFASTA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/check_seq_frag_in_MSAclustal_intact_viaFASTA.py -------------------------------------------------------------------------------- /alignment-utilities/check_seq_in_MSAclustal_consistent_with_FASTA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/check_seq_in_MSAclustal_consistent_with_FASTA.py -------------------------------------------------------------------------------- /alignment-utilities/demo roughly_score_relationships_to_subject_seq_pairwise_premsa.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/demo roughly_score_relationships_to_subject_seq_pairwise_premsa.ipynb -------------------------------------------------------------------------------- /alignment-utilities/extract_regions_from_clustal_alignment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/extract_regions_from_clustal_alignment.py -------------------------------------------------------------------------------- /alignment-utilities/mview_to_CLUSTAL.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/mview_to_CLUSTAL.py -------------------------------------------------------------------------------- /alignment-utilities/reverse_complement_of_clustal_alignment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/reverse_complement_of_clustal_alignment.py -------------------------------------------------------------------------------- /alignment-utilities/roughly_score_relationships_to_subject_seq_pairwise_premsa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/roughly_score_relationships_to_subject_seq_pairwise_premsa.py -------------------------------------------------------------------------------- /alignment-utilities/score_columns_in_clustal_msa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/score_columns_in_clustal_msa.py -------------------------------------------------------------------------------- /alignment-utilities/score_differences_between_sequences_by_pairwise_alignment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/score_differences_between_sequences_by_pairwise_alignment.py -------------------------------------------------------------------------------- /alignment-utilities/score_sequences_in_clustal_msa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/score_sequences_in_clustal_msa.py -------------------------------------------------------------------------------- /alignment-utilities/score_sequences_in_clustal_msa_favoring_top_line.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/alignment-utilities/score_sequences_in_clustal_msa_favoring_top_line.py -------------------------------------------------------------------------------- /annotation-utilities/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/annotation-utilities/README.md -------------------------------------------------------------------------------- /annotation-utilities/measure_intergenic_regions_in_mito_annotations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/annotation-utilities/measure_intergenic_regions_in_mito_annotations.py -------------------------------------------------------------------------------- /assess_coding_potential_and_changes/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/assess_coding_potential_and_changes/README.md -------------------------------------------------------------------------------- /bendit_server-utilities/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/bendit_server-utilities/README.md -------------------------------------------------------------------------------- /bendit_server-utilities/bendit_server_results_to_df.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/bendit_server-utilities/bendit_server_results_to_df.py -------------------------------------------------------------------------------- /bendit_standalone-utilities/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/bendit_standalone-utilities/README.md -------------------------------------------------------------------------------- /bendit_standalone-utilities/bendit_standalone_results_to_df.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/bendit_standalone-utilities/bendit_standalone_results_to_df.py -------------------------------------------------------------------------------- /blast-utilities/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/blast-utilities/README.md -------------------------------------------------------------------------------- /blast-utilities/blast_to_df.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/blast-utilities/blast_to_df.py -------------------------------------------------------------------------------- /blast-utilities/demo_blast2df_in_python2.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/blast-utilities/demo_blast2df_in_python2.ipynb -------------------------------------------------------------------------------- /circos-utilities/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/circos-utilities/README.md -------------------------------------------------------------------------------- /circos-utilities/UCSC_chrom_sizes_2_circos_karyotype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/circos-utilities/UCSC_chrom_sizes_2_circos_karyotype.py -------------------------------------------------------------------------------- /circos-utilities/demo UCSC_chrom_sizes_2_circos_karyotype script.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/circos-utilities/demo UCSC_chrom_sizes_2_circos_karyotype script.ipynb -------------------------------------------------------------------------------- /count_triplets/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/count_triplets/README.md -------------------------------------------------------------------------------- /count_triplets/triplet_frequency.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/count_triplets/triplet_frequency.py -------------------------------------------------------------------------------- /ena-utilities/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/ena-utilities/README.md -------------------------------------------------------------------------------- /hhsuite3-utilities/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/hhsuite3-utilities/README.md -------------------------------------------------------------------------------- /hhsuite3-utilities/core_reduction_dataframe_steps_for_ECIIIL_genome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/hhsuite3-utilities/core_reduction_dataframe_steps_for_ECIIIL_genome.py -------------------------------------------------------------------------------- /hhsuite3-utilities/hhsuite3_results_to_df.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/hhsuite3-utilities/hhsuite3_results_to_df.py -------------------------------------------------------------------------------- /hhsuite3-utilities/make_report_on_equivalents_of_interacting_residues.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/hhsuite3-utilities/make_report_on_equivalents_of_interacting_residues.py -------------------------------------------------------------------------------- /mcscan-utilities/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/mcscan-utilities/README.md -------------------------------------------------------------------------------- /mcscan-utilities/get_if_chromosome_rearranged_func_AFTER_MCscan_simplified.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/mcscan-utilities/get_if_chromosome_rearranged_func_AFTER_MCscan_simplified.py -------------------------------------------------------------------------------- /omega-presence/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/omega-presence/README.md -------------------------------------------------------------------------------- /omega-presence/check_for_omega_HEG.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/omega-presence/check_for_omega_HEG.py -------------------------------------------------------------------------------- /omega-presence/check_for_omega_intron.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/omega-presence/check_for_omega_intron.py -------------------------------------------------------------------------------- /omega-presence/find_mito_fungal_lsu_rRNA_and_check_for_omega_intron.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/omega-presence/find_mito_fungal_lsu_rRNA_and_check_for_omega_intron.py -------------------------------------------------------------------------------- /patmatch-utilities/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/patmatch-utilities/README.md -------------------------------------------------------------------------------- /patmatch-utilities/matches_a_patmatch_pattern.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/patmatch-utilities/matches_a_patmatch_pattern.py -------------------------------------------------------------------------------- /patmatch-utilities/patmatch_results_to_df.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/patmatch-utilities/patmatch_results_to_df.py -------------------------------------------------------------------------------- /plot_expression_across_chromosomes/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_expression_across_chromosomes/LICENSE -------------------------------------------------------------------------------- /plot_expression_across_chromosomes/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_expression_across_chromosomes/README.md -------------------------------------------------------------------------------- /plot_expression_across_chromosomes/example_imgs/genes_mean_TPM_across_chr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_expression_across_chromosomes/example_imgs/genes_mean_TPM_across_chr.png -------------------------------------------------------------------------------- /plot_expression_across_chromosomes/example_imgs/genes_mean_TPM_across_chr_IV_VIII_XII.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_expression_across_chromosomes/example_imgs/genes_mean_TPM_across_chr_IV_VIII_XII.png -------------------------------------------------------------------------------- /plot_expression_across_chromosomes/example_imgs/genes_mean_TPM_across_chr_smooth.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_expression_across_chromosomes/example_imgs/genes_mean_TPM_across_chr_smooth.png -------------------------------------------------------------------------------- /plot_expression_across_chromosomes/example_imgs/genes_mean_TPM_across_chrlines.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_expression_across_chromosomes/example_imgs/genes_mean_TPM_across_chrlines.png -------------------------------------------------------------------------------- /plot_expression_across_chromosomes/example_imgs/genes_mean_TPM_across_chrnolog.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_expression_across_chromosomes/example_imgs/genes_mean_TPM_across_chrnolog.png -------------------------------------------------------------------------------- /plot_expression_across_chromosomes/example_imgs/real_data_no_anueploidy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_expression_across_chromosomes/example_imgs/real_data_no_anueploidy.png -------------------------------------------------------------------------------- /plot_expression_across_chromosomes/plot_expression_across_chromosomes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_expression_across_chromosomes/plot_expression_across_chromosomes.py -------------------------------------------------------------------------------- /plot_expression_across_chromosomes/plot_expression_across_chromosomes_direct.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_expression_across_chromosomes/plot_expression_across_chromosomes_direct.py -------------------------------------------------------------------------------- /plot_nt_imbalance/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_nt_imbalance/README.md -------------------------------------------------------------------------------- /plot_nt_imbalance/imblance_plot_exmple.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_nt_imbalance/imblance_plot_exmple.png -------------------------------------------------------------------------------- /plot_nt_imbalance/nucleotide_difference_imbalance_plot_stylized_like_Figure_8_of_Morrill_et_al_2016.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_nt_imbalance/nucleotide_difference_imbalance_plot_stylized_like_Figure_8_of_Morrill_et_al_2016.py -------------------------------------------------------------------------------- /plot_nt_imbalance/two_nucleotides_in_proximity_difference_imbalance_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_nt_imbalance/two_nucleotides_in_proximity_difference_imbalance_plot.py -------------------------------------------------------------------------------- /plot_read_data/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_read_data/README.md -------------------------------------------------------------------------------- /plot_read_data/plot_5prime_end_from_bedgraph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_read_data/plot_5prime_end_from_bedgraph.py -------------------------------------------------------------------------------- /plot_read_data/plot_coverage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_read_data/plot_coverage.py -------------------------------------------------------------------------------- /plot_read_data/plot_coverage_and_starts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_read_data/plot_coverage_and_starts.py -------------------------------------------------------------------------------- /plot_sites/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_sites/README.md -------------------------------------------------------------------------------- /plot_sites/plot_sites_example_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_sites/plot_sites_example_plot.png -------------------------------------------------------------------------------- /plot_sites/plot_sites_position_across_chromosome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fomightez/sequencework/HEAD/plot_sites/plot_sites_position_across_chromosome.py --------------------------------------------------------------------------------