List of Programs¶
Below is a list, by function (directory), of the various programs included in
the * phyluce package. This list includes ALL programs in phyluce, and some may
be lightly tested. This list of programs does not include programs
currently in the ATTIC
directory of the repository, because these programs
are deprecated.
assembly¶
- phyluce_assembly_assemblo_abyss
- phyluce_assembly_assemblo_trinity
- phyluce_assembly_assemblo_velvet
- phyluce_assembly_copy_trinity_symlinks
- phyluce_assembly_explode_get_fastas_file
- phyluce_assembly_extract_contigs_to_barcodes
- phyluce_assembly_get_fasta_lengths
- phyluce_assembly_get_fastas_from_match_counts
- phyluce_assembly_get_fastq_lengths
- phyluce_assembly_get_match_counts
- phyluce_assembly_get_trinity_coverage
- phyluce_assembly_get_trinity_coverage_for_uce_loci
- phyluce_assembly_match_contigs_to_barcodes
- phyluce_assembly_match_contigs_to_probes
- phyluce_assembly_parse_trinity_coverage_for_uce_loci_log
- phyluce_assembly_parse_trinity_coverage_log
- phyluce_assembly_screen_probes_for_dupes
align¶
- phyluce_align_add_missing_data_designators
- phyluce_align_convert_one_align_to_another
- phyluce_align_explode_alignments
- phyluce_align_extract_taxa_from_alignments
- phyluce_align_extract_taxon_fasta_from_alignments
- phyluce_align_filter_alignments
- phyluce_align_filter_characters_from_alignments
- phyluce_align_format_concatenated_phylip_for_paml
- phyluce_align_format_nexus_files_for_mrbayes
- phyluce_align_format_nexus_files_for_raxml
- phyluce_align_get_align_summary_data
- phyluce_align_get_bed_from_lastz
- phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed
- phyluce_align_get_incomplete_matrix_estimates
- phyluce_align_get_indels_from_alignments
- phyluce_align_get_informative_sites
- phyluce_align_get_only_loci_with_min_taxa
- phyluce_align_get_smilogram_from_alignments
- phyluce_align_get_taxon_locus_counts_in_alignments
- phyluce_align_get_trimmed_alignments_from_untrimmed
- phyluce_align_move_align_by_conf_file
- phyluce_align_output_list_of_taxon_counts
- phyluce_align_parallel_sate
- phyluce_align_randomly_sample_and_concatenate
- phyluce_align_remove_empty_taxa
- phyluce_align_remove_locus_name_from_nexus_lines
- phyluce_align_screen_alignments_for_problems
- phyluce_align_seqcap_align
- phyluce_align_split_concat_nexus_to_loci
genetrees¶
- phyluce_genetrees_phybase
- phyluce_genetrees_reformat_raxml_output
- phyluce_genetrees_rename_tree_leaves
- phyluce_genetrees_run_raxml_bootstraps
- phyluce_genetrees_run_raxml_genetrees
- phyluce_genetrees_run_raxml_multilocus_bootstraps
- phyluce_genetrees_split_models_from_genetrees
ncbi¶
- phyluce_ncbi_chunk_fasta_for_ncbi
- phyluce_ncbi_example-prep.conf
- phyluce_ncbi_prep_uce_align_files_for_ncbi
- phyluce_ncbi_prep_uce_fasta_files_for_ncbi
snps¶
- phyluce_snp_bwa_align
- phyluce_snp_convert_vcf_to_snapp
- phyluce_snp_convert_vcf_to_structure
- phyluce_snp_find_snps_in_bed_interval
- phyluce_snp_get_dbsnp_freq_stats
- phyluce_snp_get_dbsnp_variability_for_all_uces
- phyluce_snp_prep_interval_list_file_for_picard
- phyluce_snp_screen_vcf_files
- phyluce_snp_summarize_vcf_file
utilities¶
- phyluce_utilities_combine_reads
- phyluce_utilities_filter_bed_by_fasta
- phyluce_utilities_merge_multiple_gzip_files
- phyluce_utilities_merge_next_seq_gzip_files
- phyluce_utilities_replace_many_links
- phyluce_utilities_sample_reads_from_files
- phyluce_utilities_unmix_fasta_reads
probes¶
- phyluce_probe_easy_lastz
- phyluce_probe_get_clusters_from_bed
- phyluce_probe_get_clusters_from_taxa
- phyluce_probe_get_genome_sequences_from_bed
- phyluce_probe_get_locus_bed_from_lastz_files
- phyluce_probe_get_multi_fasta_table
- phyluce_probe_get_multi_merge_table
- phyluce_probe_get_probe_bed_from_lastz_files
- phyluce_probe_get_screened_loci_by_proximity
- phyluce_probe_get_subsets_of_tiled_probes
- phyluce_probe_get_tiled_probe_from_multiple_inputs
- phyluce_probe_get_tiled_probes
- phyluce_probe_query_multi_fasta_table
- phyluce_probe_query_multi_merge_table
- phyluce_probe_remove_duplicate_hits_from_probes_using_lastz
- phyluce_probe_remove_overlapping_probes_given_config
- phyluce_probe_run_multiple_lastzs_sqlite
- phyluce_probe_slice_sequence_from_genomes
- phyluce_probe_strip_masked_loci_from_set