GitHub - philipwoods/scripts-bio: Assorted bioinformatics scripts

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 85 Commits
.gitignore		.gitignore
BLAST-viewer.py		BLAST-viewer.py
GFFParser.py		GFFParser.py
add-info-to-fasta.sh		add-info-to-fasta.sh
add-info-to-gff3.py		add-info-to-gff3.py
align-individual-marker-genes.sh		align-individual-marker-genes.sh
anvi-run-emapper.sh		anvi-run-emapper.sh
anvi-run-fegenie.sh		anvi-run-fegenie.sh
anvi-script-align-genes-by-id.py		anvi-script-align-genes-by-id.py
anvi-script-alignment-enrichment.sh		anvi-script-alignment-enrichment.sh
anvi-script-export-locus-batch.sh		anvi-script-export-locus-batch.sh
anvi-script-extract-prot-motifs.sh		anvi-script-extract-prot-motifs.sh
anvi-script-extract-synteny-groups.sh		anvi-script-extract-synteny-groups.sh
anvi-script-frequency-enrichment.sh		anvi-script-frequency-enrichment.sh
anvi-script-get-annotated-genome.sh		anvi-script-get-annotated-genome.sh
anvi-script-get-cog-category-frequencies.sh		anvi-script-get-cog-category-frequencies.sh
anvi-script-get-sequences-by-function.sh		anvi-script-get-sequences-by-function.sh
anvi-script-get-sequences-by-id.sh		anvi-script-get-sequences-by-id.sh
anvi-script-prep-clinker.sh		anvi-script-prep-clinker.sh
calculate-aai.py		calculate-aai.py
clean-gff-products.sh		clean-gff-products.sh
concatenate-gene-alignments.py		concatenate-gene-alignments.py
consolidate-series.py		consolidate-series.py
convert-sequence.py		convert-sequence.py
deduplicate-synteny.py		deduplicate-synteny.py
evaluate_alignment.py		evaluate_alignment.py
evaluate_qa.py		evaluate_qa.py
fegenie_convert_table.py		fegenie_convert_table.py
fegenie_modify_deflines.py		fegenie_modify_deflines.py
filter-alignment.py		filter-alignment.py
filter-coinfinder-pairs.py		filter-coinfinder-pairs.py
filter-fasta.py		filter-fasta.py
filter_gc_table.py		filter_gc_table.py
find-hemec-beta-barrels.sh		find-hemec-beta-barrels.sh
find_fasta_duplicate_ids.py		find_fasta_duplicate_ids.py
find_fasta_duplicate_seqs.py		find_fasta_duplicate_seqs.py
finish-alphafold.sh		finish-alphafold.sh
finish-tmhmm.sh		finish-tmhmm.sh
fix_functional_occurrence_table.py		fix_functional_occurrence_table.py
format-enrichment-input.py		format-enrichment-input.py
gen-anvi-external-genomes.py		gen-anvi-external-genomes.py
gen-artemis-project.py		gen-artemis-project.py
get-seq-lengths.py		get-seq-lengths.py
get-sequence-by-coordinates.py		get-sequence-by-coordinates.py
get-sequences-by-coordinates.sh		get-sequences-by-coordinates.sh
get_ncbi_names.py		get_ncbi_names.py
gff_to_genbank.py		gff_to_genbank.py
modify_fasta_defline.py		modify_fasta_defline.py
parse-alignment-column-frequencies.py		parse-alignment-column-frequencies.py
parse-cog-cat-functions.py		parse-cog-cat-functions.py
parse-function-frequency.py		parse-function-frequency.py
parse-paml-rst.py		parse-paml-rst.py
pili-conductivity-tester.py		pili-conductivity-tester.py
pretty-print.py		pretty-print.py
prot_motif_count.pl		prot_motif_count.pl
prot_motif_search.pl		prot_motif_search.pl
reformat-anvio-gc-deflines.py		reformat-anvio-gc-deflines.py
reformat-anvio-hmm-deflines.py		reformat-anvio-hmm-deflines.py
reformat-jalview-conservation.py		reformat-jalview-conservation.py
refseq_exclusion.py		refseq_exclusion.py
rename_ncbi_genomes.py		rename_ncbi_genomes.py
revcomp.py		revcomp.py
run-kegg-decoder.sh		run-kegg-decoder.sh
separate-marker-genes.py		separate-marker-genes.py
sort-fasta.py		sort-fasta.py
split-fasta.py		split-fasta.py
summarize-gc-functions.py		summarize-gc-functions.py
summarize-loci.py		summarize-loci.py
translate-sequence.py		translate-sequence.py
truncate_sequence.py		truncate_sequence.py