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