GitHub - berkeleyphylogenomics/BPG_utilities: miscellaneous utilities written by berkeley phylogenomics group members

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 6 Commits
bpg		bpg
pfacts003		pfacts003
static		static
Ktreedist.pl		Ktreedist.pl
README.md		README.md
align_nj_to_align_ml.py		align_nj_to_align_ml.py
align_originals_via_shmms_and_score.py		align_originals_via_shmms_and_score.py
align_pdb_hits_to_hmm.py		align_pdb_hits_to_hmm.py
align_using_input_msa.py		align_using_input_msa.py
alignedfasta_to_unalignedfasta.py		alignedfasta_to_unalignedfasta.py
alignhits.pl		alignhits.pl
alignments_lib.py		alignments_lib.py
amap-multipw.py		amap-multipw.py
bin_fasta_for_flowerpower.py		bin_fasta_for_flowerpower.py
buildFamily.py		buildFamily.py
build_and_score_models_for_pair.py		build_and_score_models_for_pair.py
build_ghmm.py		build_ghmm.py
build_hhalign_kerf_shmms.py		build_hhalign_kerf_shmms.py
build_hmmer3_hmm_from_alignment.py		build_hmmer3_hmm_from_alignment.py
build_hmmer_hmm_from_alignment_8cpus.py		build_hmmer_hmm_from_alignment_8cpus.py
build_infoshare_kerf_shmms.py		build_infoshare_kerf_shmms.py
build_model.py		build_model.py
build_models.py		build_models.py
build_models_for_target.py		build_models_for_target.py
build_one_model.py		build_one_model.py
build_w05_kerf_shmms.py		build_w05_kerf_shmms.py
buildali.pl		buildali.pl
casp_create_hmms.py		casp_create_hmms.py
casp_non_matchmaker_align.py		casp_non_matchmaker_align.py
casp_shmm_alignment.py		casp_shmm_alignment.py
cattrees.py		cattrees.py
cleanss2.pl		cleanss2.pl
cleanss2.py		cleanss2.py
clustalw-multipw.py		clustalw-multipw.py
collect_tsvmod_scores_for_pair.py		collect_tsvmod_scores_for_pair.py
compress_alignment.py		compress_alignment.py
compress_alignments_for_pair.py		compress_alignments_for_pair.py
compute_alignment_conservation.py		compute_alignment_conservation.py
compute_all_q_combined_scores.py		compute_all_q_combined_scores.py
compute_all_signals.py		compute_all_signals.py
compute_q_combined_score.py		compute_q_combined_score.py
compute_ss_score.py		compute_ss_score.py
compute_ss_score_ruchira.py		compute_ss_score_ruchira.py
concat_for_multipw.py		concat_for_multipw.py
consensus_alignments.py		consensus_alignments.py
convert.pl		convert.pl
convert_pairwise_orthoxml_to_text.py		convert_pairwise_orthoxml_to_text.py
count_pairwise_alignments_for_pair.py		count_pairwise_alignments_for_pair.py
create_hmms.py		create_hmms.py
crop_to_seed.py		crop_to_seed.py
csv_to_html_table.py		csv_to_html_table.py
dir_of_family.py		dir_of_family.py
discern.py		discern.py
do_kerf.py		do_kerf.py
dssp2seq.py		dssp2seq.py
dssp_to_threestate.py		dssp_to_threestate.py
evaluate_secondary_structure_prediction.py		evaluate_secondary_structure_prediction.py
extract_orthologs.py		extract_orthologs.py
extract_pdbs_and_target_from_msa.py		extract_pdbs_and_target_from_msa.py
extract_pfam_subsequence.pl		extract_pfam_subsequence.pl
extract_relevant_features.pl		extract_relevant_features.pl
extract_unaligned_subsequence_matching_pfam_domain.py		extract_unaligned_subsequence_matching_pfam_domain.py
family_names_from_sqlite.py		family_names_from_sqlite.py
fatcat-1.py		fatcat-1.py
filter_out_dna.py		filter_out_dna.py
find_taxonomic_distribution.py		find_taxonomic_distribution.py
find_thresholded_phogs_django.py		find_thresholded_phogs_django.py
flowerpower.pl		flowerpower.pl
flowerpower_old.pl		flowerpower_old.pl
fp_top_by_pwid_with_seed.py		fp_top_by_pwid_with_seed.py
generateDS.py		generateDS.py
generateds_gui.py		generateds_gui.py
getUniverseFromMSA.py		getUniverseFromMSA.py
get_blastable_database_parameters.py		get_blastable_database_parameters.py
get_pdb_single_chain.py		get_pdb_single_chain.py
get_yl_per_pair.py		get_yl_per_pair.py
getdir_alignment.py		getdir_alignment.py
greedily_cover_pfam_domain_with_phylofacts_families.py		greedily_cover_pfam_domain_with_phylofacts_families.py
hhalign_with_hmms.py		hhalign_with_hmms.py
identify_subfamily_of_sequence.py		identify_subfamily_of_sequence.py
incorporate_branch_lengths_from_unrooted_tree.py		incorporate_branch_lengths_from_unrooted_tree.py
insertFamilyIntoDB.py		insertFamilyIntoDB.py
insert_fasttree.py		insert_fasttree.py
integrate_features.pl		integrate_features.pl
intrepid.pl		intrepid.pl
intrepid.py		intrepid.py
label_transformed_signals.py		label_transformed_signals.py
launch_jobs_on_n_cores.py		launch_jobs_on_n_cores.py
legacy_blast.pl		legacy_blast.pl
link_gathered_homologs.py		link_gathered_homologs.py
load_uniprot.py		load_uniprot.py
long_branch_symmdiff.py		long_branch_symmdiff.py
mafft-multipw.py		mafft-multipw.py
make_ascii_ghmm.py		make_ascii_ghmm.py
make_nj_tree.py		make_nj_tree.py
make_nr_at_100_with_dict.py		make_nr_at_100_with_dict.py
make_sciphy_subfams.py		make_sciphy_subfams.py
make_superposed_pdb.py		make_superposed_pdb.py
mask_alignments.py		mask_alignments.py
midpoint_reroot.py		midpoint_reroot.py

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miscellaneous utilities written by berkeley phylogenomics group members

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