MANIFEST.in
README.md
setup.cfg
setup.py
BConverters/AnnotationConverters.py
BConverters/Converters.py
BConverters/MultipleAlignmentConverters.py
BConverters/SequenceConverters.py
BConverters/__init__.py
Data/Nucleotides.py
Data/__init__.py
Download/NCBI.py
Download/__init__.py
Functions/Generators.py
Functions/__init__.py
GeneSynonyms/MitoGenesSynonyms.py
GeneSynonyms/__init__.py
Graphics/Plots.py
Graphics/__init__.py
MAVR.egg-info/PKG-INFO
MAVR.egg-info/SOURCES.txt
MAVR.egg-info/dependency_links.txt
MAVR.egg-info/requires.txt
MAVR.egg-info/top_level.txt
Parsers/CCF.py
Parsers/GFF.py
Parsers/__init__.py
Pictures/Draw.py
Pictures/__init__.py
Pictures/Features/Abstract.py
Pictures/Features/Protein.py
Pictures/Features/__init__.py
Pictures/Styles/Features.py
Pictures/Styles/__init__.py
Pipelines/Abstract.py
Pipelines/Alignment.py
Pipelines/DiffExpression.py
Pipelines/Filtering.py
Pipelines/Phylogeny.py
Pipelines/Primers.py
Pipelines/SNPCall.py
Pipelines/Sanger.py
Pipelines/__init__.py
Pipelines/Expansion/__init__.py
Pipelines/GenomeAnnotation/ProteinCodingGeneAnnotation.py
Pipelines/GenomeAnnotation/RepeatAnnotation.py
Pipelines/GenomeAnnotation/__init__.py
Pipelines/GenomeAssembly/Assembly.py
Pipelines/GenomeAssembly/ContigAssembly.py
Pipelines/GenomeAssembly/GapClosing.py
Pipelines/GenomeAssembly/Scaffolding.py
Pipelines/GenomeAssembly/__init__.py
Pipelines/TenX/Alignment.py
Pipelines/TenX/__init__.py
SeqAnalysis/SeqAnalysis.py
SeqAnalysis/__init__.py
scripts/CDS_region_variants.py
scripts/blast_fastqc.py
scripts/extract_genes_from_treefam_output.py
scripts/extract_sequences.py
scripts/get_flanking_regions.py
scripts/remove_duplicates_flybase_UTR.py
scripts/1000genomes/convert_vcf_with_functional_annotation_to_table.py
scripts/10x/align_and_call_by_longranger.py
scripts/10x/prepare_reference.py
scripts/GO/extract_entries_by_GO_from_eggnogmapper_output.py
scripts/alignment/align_proteins_to_genome_by_blat.py
scripts/alignment/align_transcripts_to_genome_by_blat.py
scripts/alignment/alignment_pipeline.py
scripts/alignment/analize_collapsed_coverage_file.py
scripts/alignment/check_read_pairing_in_name_sorted_bam.sh
scripts/alignment/collapse_bedgraph.py
scripts/alignment/collapse_bedtools_coverage_file.sh
scripts/alignment/collapse_per_base_covarage_mask.py
scripts/alignment/convert_per_base_coverage_file_to_vcf.py
scripts/alignment/convert_picard_dict_to_syn_file.py
scripts/alignment/create_mappability_map_by_gem.py
scripts/alignment/draw_insert_size_distribution.py
scripts/alignment/extract_data_for_cds_from_collapsed_coverage_file.py
scripts/alignment/extract_fastq_from_bam.py
scripts/alignment/extract_se_from_bam.sh
scripts/alignment/filter_psl_by_ids.py
scripts/alignment/generate_mask_from_coverage_files.py
scripts/alignment/get_bam_coverage_stats.py
scripts/alignment/get_read_names_from_sam.py
scripts/alignment/get_reads_by_name.py
scripts/alignment/get_stats_from_coverage_file.py
scripts/alignment/map_reads.py
scripts/alignment/mark_duplicates.py
scripts/alignment/parallel_blat.py
scripts/alignment/parallel_exonerate.py
scripts/alignment/remove_duplicates_and_poorly_aligned_reads.py
scripts/alignment/sam2bam
scripts/alignment/blast/MASKED_BLAST_DB
scripts/alignment/blast/blast_all_vs_all.py
scripts/alignment/blast/extract_hits_from_blast_tblout.py
scripts/alignment/blast/filter_blast_output_by_ids.py
scripts/alignment/blast/filter_blast_output_by_parameters.py
scripts/alignment/blast/get_query_target_from_blast_output.sh
scripts/alignment/blast/get_top_hits_from_blast_output.sh
scripts/alignment/blast/make_blastplus_db.py
scripts/alignment/blast/nt_nr_blast_output_analysis.py
scripts/alignment/blast/parallel_blast_commands.py
scripts/annotation/add_gene_synonyms_snpeff_table.py
scripts/annotation/add_len_to_simple_output.py
scripts/annotation/annotate_vcf.py
scripts/annotation/assign_synonyms_to_annotations_from_augustus_gff.py
scripts/annotation/assign_synonyms_to_features_from_augustus_gff.py
scripts/annotation/count_features_per_scaffold.py
scripts/annotation/distances_between_genes.py
scripts/annotation/draw_evidence_figures.py
scripts/annotation/extract_annotations_from_gff_by_ids.py
scripts/annotation/extract_annotations_from_gff_by_types.py
scripts/annotation/extract_cds_by_gff.py
scripts/annotation/extract_evidence_by_ids.py
scripts/annotation/extract_exon_lengths_from_genbank_file.py
scripts/annotation/extract_features_with_subfeatures_from_gff.py
scripts/annotation/extract_genes_from_exonerate_output_by_ids.py
scripts/annotation/extract_introns_from_genbank.py
scripts/annotation/extract_longest_isoforms_from_evidence_file.py
scripts/annotation/extract_longest_isoforms_from_gff.py
scripts/annotation/extract_proteins_from_augustus_output.py
scripts/annotation/extract_transcripts_from_gff_by_ids.py
scripts/annotation/find_PAS.py
scripts/annotation/find_single_exon_genes.py
scripts/annotation/fix_absent_feature_type.py
scripts/annotation/fix_gff_coordinates.py
scripts/annotation/gather_protein-coding_gene-stats_from_gff.py
scripts/annotation/get_isoform_len_from_gff.py
scripts/annotation/get_scaffold_ids_from_gff.py
scripts/annotation/get_summary_table.py
scripts/annotation/get_transcript_len_from_gff.py
scripts/annotation/get_transcript_to_pep_accordance_from_gtf.py
scripts/annotation/gff_examine.py
scripts/annotation/merge_overlapping_feature_in_simple_format.py
scripts/annotation/parallel_augustus.py
scripts/annotation/parallel_augustus_tmp.py
scripts/annotation/prepare_intron_hints_from_STAR_junction_file.py
scripts/annotation/replace_augustus_ids.py
scripts/annotation/replace_augustus_ids_by_synonyms.py
scripts/annotation/replace_region_names_in_gff.py
scripts/annotation/trim_cds_and_remove_terminal_stop_codons.py
scripts/annotation/VEP/prepare_gff.py
scripts/annotation/accordance/add_length_to_accordance_file.py
scripts/annotation/augustus/add_exon_lines_to_augustus_gff.py
scripts/annotation/augustus/exonerate2hints.pl
scripts/annotation/augustus/exonerate2hints_with_utrs.pl
scripts/annotation/augustus/join_hints.py
scripts/annotation/ensembl/correct_ensembl_genbank_files.sh
scripts/annotation/ensembl/get_gene_transcript_protein_from_ensembl_pep_fasta.py
scripts/annotation/ensembl/get_longest_pep_per_gene_from_ensembl_pep_file.py
scripts/annotation/exonerate/extract_top_hits_from_target_gff_exonerate.py
scripts/annotation/exonerate/get_query_ids_from_exonerate_output.bash
scripts/annotation/exonerate/parallel_exonerate.py
scripts/annotation/exonerate/prepare_annotation_file_from_transcript_and_cds.py
scripts/annotation/exonerate/prepare_hints_from_exonerate_target_output.py
scripts/annotation/exonerate/prepare_hints_from_splited_exonerate_target_output.py
scripts/annotation/exonerate/split_exonerate_output.py
scripts/annotation/genescope/extract_gene_type_from_genoscope_gff.bash
scripts/annotation/gff/add_alias_to_feature_in_gff.py
scripts/annotation/gff/add_flanks_to_gff_record.py
scripts/annotation/gff/convert_bed_to_gff.py
scripts/annotation/gff/convert_gff_to_simple_bed.py
scripts/annotation/gff/count_total_feature_length.py
scripts/annotation/gff/extract_gff_records_by_description_value.py
scripts/annotation/gff/extract_transcripts_by_gff.py
scripts/annotation/gff/get_feature_length_distribution.py
scripts/annotation/gff/get_feature_to_parent_correspondence_from_gff.py
scripts/annotation/gff/get_features_from_gff.py
scripts/annotation/gff/rename_scaffolds_in_gff.py
scripts/annotation/gff/sort_gff.bash
scripts/annotation/ncbi/add_protein_length_to_accordance_file.py
scripts/annotation/ncbi/analyze_ncbi_pep.py
scripts/annotation/ncbi/extract_gene_info_from_ncbi_gff.py
scripts/annotation/ncbi/get_cds_for_proteins.py
scripts/annotation/ncbi/get_gene_to_protein_accordance_from_gff.bash
scripts/annotation/ncbi/get_longest_proteins_from_protein_tab_file.py
scripts/annotation/ncbi/rename_genome_files.py
scripts/annotation/rRNA/analyze_barrnap_report.py
scripts/annotation/rRNA/annotate_rrna_by_barrnap.py
scripts/annotation/test/check_chunks.py
scripts/antibodies/check_for_bad_antigen_candidates.py
scripts/assembly/busco.py
scripts/assembly/compare_busco_results.py
scripts/assembly/get_insert_size_distribution.py
scripts/assembly/get_stats_from_assemblies.py
scripts/chemidoc/convert_scn_to_tiff.py
scripts/convert/convert_bedgraph_to_gff.py
scripts/convert/convert_sequences.py
scripts/convert/fasta2paml.py
scripts/convert/fasta2phylip.py
scripts/convert/fastq2fasta.sh
scripts/convert/genbank2fasta.py
scripts/convert/sequence2fastq.py
scripts/download/download_from_sra_by_fastq_dump.sh
scripts/download/download_from_sra_by_ids.py
scripts/download/download_from_sra_by_ids_by_axel.py
scripts/download/parallel_wget.py
scripts/draw/draw_barplot.py
scripts/draw/draw_chromosomes_with_features_simple.py
scripts/draw/draw_double_histogram.py
scripts/draw/draw_heatmap.py
scripts/draw/draw_histogram.py
scripts/draw/draw_histogram_from_multiple_files.py
scripts/draw/draw_percent_histogram.py
scripts/draw/draw_plot.py
scripts/draw/draw_protein_alignment.py
scripts/draw/draw_tetra_histogram_with_two_logscaled.py
scripts/draw/draw_venn_histogram.py
scripts/draw/test_colormap.py
scripts/ensembl/convert_biomart_protein_annotation_to_gff.py
scripts/entrez/count_assemblies_from_genome_summaries.sh
scripts/entrez/get_gene_sequences.py
scripts/entrez/get_subtaxa_for_taxa.py
scripts/entrez/get_taxa_genomes_summary.py
scripts/entrez/get_taxonomy.py
scripts/evolution/bootstrap_alignment.py
scripts/evolution/combine_ds_dn_w_from_bootstrap_data.py
scripts/evolution/divergence_time_estimation.py
scripts/evolution/divergence_time_estimation_all_clock.py
scripts/evolution/extract_trees_from_codeml_output.py
scripts/evolution/generate_ctl_file_for_mcmctree.py
scripts/evolution/parallel_codeml.py
scripts/evolution/parallel_extraction_of_conservative_blocks.py
scripts/evolution/parallel_positive_selection_test.py
scripts/evolution/prepare_alignment_for_codeml.py
scripts/evolution/split_paml_bootstrap_samples.py
scripts/fastq/count_reads_and_bases_in_fastq.py
scripts/fastq/count_reads_in_tiles_in_fastq.py
scripts/fastq/fastq2fasta.py
scripts/fastq/find_tiles_in_fastq.py
scripts/fastq/remove_tiles_from_fastq.py
scripts/fastq/reverse_complement_fastq.py
scripts/fastq/split_illumina_fastq_by_lanes.py
scripts/file/add_new_column_by_key_column.py
scripts/file/combine_chunks.py
scripts/file/combine_file_with_header.py
scripts/file/combine_syn_files.py
scripts/file/count_column_values.py
scripts/file/exchange_key_and_value_in_syn_file.py
scripts/file/extract_by_column_value.py
scripts/file/get_column_value_set.py
scripts/file/label_column_in_file.py
scripts/file/remove_by_column_value.py
scripts/file/remove_empty_files_in_dir.bash
scripts/file/replace_column_value_by_syn.py
scripts/file/split_file_by_column.py
scripts/file/transpose_file.sh
scripts/filter/check_fastq_presense.py
scripts/filter/draw_fraction_of_retained_pairs_per_tile_histogram.py
scripts/filter/fastqc_check.py
scripts/filter/filter_by_cookiecutter_per_lane.py
scripts/filter/filter_by_mean_quality_per_lane.py
scripts/filter/filter_by_trim_galore.py
scripts/filter/filter_by_trimmomatic.py
scripts/filter/filter_by_trimmomatic_per_lane.py
scripts/filter/filtering_mirna_pipeline.py
scripts/filter/filtering_pipeline.py
scripts/filter/gather_filtering_stats.py
scripts/filter/gather_trimmomatic_statistics.py
scripts/filter/get_general_stats_from_coockiecutter_reports.py
scripts/filter/get_general_stats_from_facut_reports.py
scripts/filter/left_clustered_starts.py
scripts/filter/merge_and_check_reads.py
scripts/filter/merge_and_filter_reads.sh
scripts/filter/merge_reads.sh
scripts/filter/remove_optical_duplicates_by_clumpify.py
scripts/filter/remove_terminal_ns.py
scripts/filter/restore_pairs.py
scripts/filter/trim_by_stirka.py
scripts/general/collaps_synonym_strings.py
scripts/general/combine_ids.py
scripts/general/combine_tables_from_file.py
scripts/general/merge_files_by_columns.py
scripts/general/parallel_md5sum.bash
scripts/graph/draw_graph.py
scripts/hmmer3/assign_sequences_to_clusters.py
scripts/hmmer3/convert_top_hits_to_families.py
scripts/hmmer3/extract_hits_by_query_ids.py
scripts/hmmer3/extract_hits_from_hmm_output.py
scripts/hmmer3/extract_hits_from_hmmer_domtblout.py
scripts/hmmer3/extract_top_hits.py
scripts/hmmer3/extract_top_hits_from_hmm_output.py
scripts/hmmer3/get_clusters_from_top_hits.py
scripts/hmmer3/get_ids_from_hmm3.py
scripts/hmmer3/parallel_hmmscan.py
scripts/install/circos_dependencies.bash
scripts/kmer/draw_kmer_distribution.py
scripts/kmer/draw_kmer_distribution_from_fastq.py
scripts/kmer/draw_kmer_distribution_from_histo.py
scripts/kmer/get_kmer_list.py
scripts/math/adjust_pvalues.py
scripts/math/get_per_row_stats_for_table_from_file.py
scripts/math/get_stats_from_numer_data.py
scripts/mtDNA/get_general_data_from_genbank_file.py
scripts/mtDNA/iterative_assembly.py
scripts/mtDNA/split_mtdna_by_genes.py
scripts/multiple_alignment/call_variants_from_alignment.py
scripts/multiple_alignment/count_dNdS_by_reference_seq_in_codon_alignment.py
scripts/multiple_alignment/count_unique_positions_per_sequence.py
scripts/multiple_alignment/draw_alignment_stats_distributions.py
scripts/multiple_alignment/extract_codon_positions.py
scripts/multiple_alignment/extract_degenerate_sites_from_codon_alignment.py
scripts/multiple_alignment/extract_parsimony_informative_sites_from_alignment.py
scripts/multiple_alignment/extract_sequences_from_alignment.py
scripts/multiple_alignment/extract_substitutions.py
scripts/multiple_alignment/extract_variable_sites_from_alignment.py
scripts/multiple_alignment/fasta_align2seq.bash
scripts/multiple_alignment/gather_alignment_stats.py
scripts/multiple_alignment/get_codon_alignment.py
scripts/multiple_alignment/get_distribution_of_unique_positions_in_alignments.py
scripts/multiple_alignment/get_position_precence_matrix.py
scripts/multiple_alignment/get_specific_positions_from_alignment.py
scripts/multiple_alignment/get_specific_positions_from_multiple_alignments.py
scripts/multiple_alignment/merge_alignments.py
scripts/multiple_alignment/parallel_codon_alignment_by_guidance2.py
scripts/multiple_alignment/parallel_codon_alignment_by_prank.py
scripts/multiple_alignment/parallel_mafft.py
scripts/multiple_alignment/parallel_prank.py
scripts/multiple_alignment/remove_columns_with_gaps.py
scripts/multiple_alignment/slice_multiple_alignment.py
scripts/multiple_alignment/translate_codon_alignment.py
scripts/pacbio/pacbio_adapters_tag.bash
scripts/phylogenetics/add_features_to_tree.py
scripts/phylogenetics/collapse_by_support.py
scripts/phylogenetics/convert_trees.py
scripts/phylogenetics/draw_tree.py
scripts/phylogenetics/draw_tree_with_features.py
scripts/phylogenetics/extract_node_names.py
scripts/phylogenetics/get_leave_names_from_trees.py
scripts/phylogenetics/prune_tree.py
scripts/phylogenetics/remove_nodes_by_ids.py
scripts/phylogenetics/rename_nodes.py
scripts/phylogenetics/split_by_children.py
scripts/phylogenetics/unroot_tree.py
scripts/population/convert_block_det_file_to_gff.py
scripts/population/extract_sequences_from_plink_binary_data.py
scripts/population/test_plink_roh_parameters.py
scripts/population/psmc/plot_psmc.py
scripts/primers/filter_degeprime_output.py
scripts/primers/generate_primers_for_mtDNA_amplification.py
scripts/primers/generate_str_primers.py
scripts/primers/generate_str_primers_using_flanked_trf_gff.py
scripts/primers/get_alignments.py
scripts/primers/prepare_kmer_lists_for_primer3.py
scripts/primers/remove_bad_records_from_primer3_output.py
scripts/project/init_data_dirs.bash
scripts/project/init_project_dirs.py
scripts/repeatmasking/annotate_repeats_de_novo.py
scripts/repeatmasking/annotate_repeats_for_wga.py
scripts/repeatmasking/convert_rm_out_to_gff.py
scripts/repeatmasking/convert_trf_report.py
scripts/repeatmasking/extract_repeat_classes_from_gff.py
scripts/repeatmasking/extract_repeats_for_gene_annotation_from_repeatmasker_output.py
scripts/repeatmasking/extract_repeats_from_repbase.py
scripts/repeatmasking/filter_trf_gff.py
scripts/repeatmasking/filter_trf_gff_by_exact_copy_number.py
scripts/repeatmasking/find_homopolymers.py
scripts/repeatmasking/find_homopolymers_ver2.py
scripts/repeatmasking/mask_long_tandems.py
scripts/repeatmasking/mask_repeats_for_gene_annotation_from_gff.py
scripts/repeatmasking/tandem_repeat_masking.py
scripts/repeatmasking/windowmasker_repeat_masking.py
scripts/sanger/handle_sanger_files.py
scripts/sequence/GC_content.py
scripts/sequence/check_cds_for_stop_codons.py
scripts/sequence/check_pairing.py
scripts/sequence/check_proteins_for_stop_codons.py
scripts/sequence/check_selenocystein_presence.py
scripts/sequence/compare_sequences.py
scripts/sequence/compare_sequences_by_length.py
scripts/sequence/convert_rna_to_dna.bash
scripts/sequence/convert_sequence_formats.py
scripts/sequence/correct_sequences.py
scripts/sequence/count_sequences_in_fasta.bash
scripts/sequence/count_softmasked_nucleotides.py
scripts/sequence/count_species.py
scripts/sequence/draw_length_pie.py
scripts/sequence/extract_groups_of_sequences.py
scripts/sequence/extract_ids_from_fasta.bash
scripts/sequence/extract_region.py
scripts/sequence/extract_sequences_by_gff.py
scripts/sequence/extract_sequences_by_ids.py
scripts/sequence/extract_sequences_by_length.py
scripts/sequence/extract_species_names_from_genbank_files.py
scripts/sequence/extract_terminal_sequences.py
scripts/sequence/fasta2correspondence.bash
scripts/sequence/filter_sequences_by_id_expression.py
scripts/sequence/find_cds_coordinates_in_transcript_by_pep.py
scripts/sequence/find_gaps.py
scripts/sequence/find_repeated_ids_in_fasta.bash
scripts/sequence/get_cds_pep_accordance.py
scripts/sequence/get_general_data_from_genbank_file.py
scripts/sequence/get_id_to_species_accordance.py
scripts/sequence/get_protein_marking_by_exons_from_genbank.py
scripts/sequence/get_random_species_sequences.py
scripts/sequence/get_sequence_ids.py
scripts/sequence/get_sequence_lengths.py
scripts/sequence/get_transcript_pep_accordance.py
scripts/sequence/histogram_length.py
scripts/sequence/label_sequences.py
scripts/sequence/leave_only_label.sh
scripts/sequence/make_fasta_by_correspondence.py
scripts/sequence/make_region_bed_file.py
scripts/sequence/number_of_sequences.py
scripts/sequence/prepare_region_list.py
scripts/sequence/remove_selenocystein_proteins.py
scripts/sequence/rename_sequence_ids.py
scripts/sequence/rename_sequence_ids_by_sequential_ones.py
scripts/sequence/replace_custom_aminoacids_by_unknown_residue.py
scripts/sequence/replace_selenocystein.py
scripts/sequence/reverse_complement.py
scripts/sequence/split_fasta.py
scripts/sequence/split_multifasta_file.py
scripts/sequence/split_sequence_by_regions.py
scripts/sequence/translate_sequences.py
scripts/sequence/trim_proteins_by_stop.py
scripts/sequence/truncate_id_after_label.py
scripts/sequence/unmask_sequences.py
scripts/sequence_clusters/create_gvf_files_from_species_gene_fam_and_gene_GO_fam.py
scripts/sequence_clusters/create_per_cluster_element_id_files.py
scripts/sequence_clusters/extract_clusters_and_elements_by_labels.py
scripts/sequence_clusters/extract_clusters_by_element_ids.py
scripts/sequence_clusters/extract_element_ids_from_fam_file.py
scripts/sequence_clusters/extract_monocluster_ids.py
scripts/sequence_clusters/extract_selected_families_from_fam_file.py
scripts/sequence_clusters/extract_sequences_by_clusters.py
scripts/sequence_clusters/extract_sequences_from_selected_clusters.py
scripts/sequence_clusters/extract_single_copy_clusters.py
scripts/sequence_clusters/label_accordance_file.sh
scripts/sequence_clusters/label_cluster_elements.py
scripts/sequence_clusters/merge_fam_files.py
scripts/sequence_clusters/remove_elements_by_ids.py
scripts/sequence_clusters/rename_elements_in_clusters.py
scripts/sequence_clusters/rename_sequence_in_clusters_by_species_name.py
scripts/sequence_clusters/replace_label_of_cluster_elements.py
scripts/sequence_clusters/split_clusters_by_element_labels.py
scripts/sequence_clusters/cdhit/convert_cdhit_clustering_file_to_fam.py
scripts/sequence_clusters/eggnog/assign_orthologs.py
scripts/sequence_clusters/eggnog/assign_orthologs_by_emapper.py
scripts/sequence_clusters/eggnog/convert_emapper_annotation_file.py
scripts/sequence_clusters/eggnog/convert_emapper_annotation_file_to_fam.py
scripts/sequence_clusters/eggnog/convert_members_tsv_to_fam.bash
scripts/sequence_clusters/eggnog/convert_members_tsv_to_fam.py
scripts/sequence_clusters/eggnog/edit_profile_names_in_fam_file.py
scripts/sequence_clusters/eggnog/extract_GO_terms_from_emapper_annotation_file.bash
scripts/sequence_clusters/eggnog/extract_eggnog_fam_by_protein_synonyms.py
scripts/sequence_clusters/eggnog/extract_eggnogmapper_annotations_by_protein_ids.py
scripts/sequence_clusters/eggnog/extract_predicted_gene_names_from_emapper_annotation_file.bash
scripts/sequence_clusters/eggnog/extract_proteins_from_alignments.py
scripts/sequence_clusters/eggnog/extract_species_ids_from_eggnog_fam.bash
scripts/sequence_clusters/eggnog/generate_sed_script_from_species_syn_file_for_species_id_replacement_by_latin_names.bash
scripts/sequence_clusters/eggnog/generate_sed_script_from_species_syn_file_for_species_id_replacement_by_latin_names_in_fam_file.bash
scripts/sequence_clusters/eggnog/get_species_from_eggnog_members_tsv.py
scripts/sequence_clusters/eggnog/rename_files_from_taxaid_to_species_name.py
scripts/sequence_clusters/eggnog/split_proteins_per_species.py
scripts/sequence_clusters/expansion/analyse_cafe_report.py
scripts/sequence_clusters/expansion/compare_clusters.py
scripts/sequence_clusters/expansion/draw_general_tree.py
scripts/sequence_clusters/expansion/expansion_analysis.py
scripts/sequence_clusters/expansion/expansion_pipeline_statistics.py
scripts/sequence_clusters/expansion/extract_families_graphs_from_hclust_input.py
scripts/sequence_clusters/expansion/extract_random_genes_from_reference_families_using_node_files.py
scripts/sequence_clusters/expansion/gather_statistics_from_comparison.py
scripts/sequence_clusters/expansion/get_common_correct_families.py
scripts/sequence_clusters/expansion/get_families_from_hclust_output.py
scripts/sequence_clusters/expansion/get_genes_from_families.py
scripts/sequence_clusters/expansion/prepare_cafe_input.py
scripts/sequence_clusters/expansion/remove_edges_by_nodes_from_hclust_input.py
scripts/sequence_clusters/expansion/split_hclust_families.py
scripts/sequence_clusters/expansion/split_hclust_output.py
scripts/sequence_clusters/expansion/test_hcluster_options.py
scripts/sequence_clusters/expansion_hmm/errors_distribution.py
scripts/sequence_clusters/expansion_hmm/find_correctly_assembled_families_in_all_species.py
scripts/sequence_clusters/treefam/add_lengths_to_fam_file.py
scripts/sequence_clusters/treefam/download_treefam_data.py
scripts/sequence_clusters/treefam/extract_families_of_species.py
scripts/sequence_clusters/treefam/extract_proteins_from_families.bash
scripts/sequence_clusters/treefam/extract_proteins_from_selected_families.py
scripts/sequence_clusters/treefam/extract_single_gene_families_from_cafe_input.py
scripts/sequence_clusters/treefam/gather_statistics_from_fam_files.py
scripts/sequence_clusters/treefam/get_cds_families.py
scripts/sequence_clusters/treefam/label_fam_file_with_species_name.sh
scripts/sequence_clusters/treefam/label_ortholog_files_with_species_name.sh
scripts/sequence_clusters/treefam/label_pep_with_species_name.bash
scripts/sequence_clusters/treefam/label_pep_with_species_name.sh
scripts/sequence_clusters/treefam/prepare_cafe_input_from_fam_files.py
scripts/snpcall/check_gvcf_integrity.py
scripts/snpcall/combine_gvcfs.py
scripts/snpcall/combine_same_sample_vcf.py
scripts/snpcall/combine_splited_gvcf_by_GATK.py
scripts/snpcall/combine_vcf.py
scripts/snpcall/compare_vcf.py
scripts/snpcall/create_gvcf_database.py
scripts/snpcall/filter_reference.py
scripts/snpcall/filter_vcf.py
scripts/snpcall/genotype_gvcfs.py
scripts/snpcall/hardfilter_variants.py
scripts/snpcall/index_variants.py
scripts/snpcall/intersect_vcf.py
scripts/snpcall/make_fasta_from_vcf.py
scripts/snpcall/make_fasta_from_vcf_for_regions_in_gff.py
scripts/snpcall/parallel_genotype_gvcfs.py
scripts/snpcall/parallel_gvcf_call.py
scripts/snpcall/parallel_vcf_call_gatk4.py
scripts/snpcall/prepare_reference_for_GATK.py
scripts/snpcall/remove_variants_with_filters.py
scripts/snpcall/snpcall.py
scripts/snpcall/snpcall_pipeline.py
scripts/snpcall/sort_vcf_gatk4.py
scripts/snpcall/sort_vcf_picard.py
scripts/sra/parallel_unpack_sra.py
scripts/transcriptome/align_by_star.py
scripts/transcriptome/align_miRNA_by_star.py
scripts/transcriptome/coverage_analyzis.sh
scripts/transcriptome/index_by_star.py
scripts/transcriptome/annotation/count_transcript_length_for_subread_simple_annotations.bash
scripts/transcriptome/annotation/extract_complete_proteins_from_transdecoder_output.py
scripts/transcriptome/annotation/get_cds_by_bed_from_transcript_file.py
scripts/transcriptome/annotation/predict_proteins_from_transcripts.py
scripts/transcriptome/annotation/transdecoder_annotation_analysis.bash
scripts/transcriptome/differential_expression/calculate_fpkm_for_count_table.py
scripts/transcriptome/differential_expression/combine_count_file.py
scripts/transcriptome/differential_expression/divide_count_by_base_level.py
scripts/transcriptome/differential_expression/divide_count_by_max_level.py
scripts/transcriptome/differential_expression/divide_count_by_several_base_level.py
scripts/transcriptome/differential_expression/star_htseq.py
scripts/transcriptome/miRNA/count_miRNA_by_subread.py
scripts/variant_annotation/extract_coordinates_from_hgmd_reports.py
scripts/wga/align_by_lastal.py
scripts/wga/create_last_db.py
scripts/wga/create_last_db_for_fast_wga.py
scripts/wga/dotplot_from_last_tab.py
scripts/wga/draw_dotplot.py
scripts/wga/extract_one_to_one_alignments.py
scripts/wga/filter_last_tab_output_by_len.py