Function reference • baitfindR

BLAST Functions relating to building and querying BLAST databases.
`build_blast_db()`	Build a BLAST database.
`blast_n()`	Run a blastn query.
`blast_p()`	Run a blastp query.
`blast_n_list()`	Run blastn on all fasta files in a folder.
`extract_blast_hits()`	Extract top blast hits from multiple blast output files
`realign_with_best_hits()`	Realign top blast hit of multi-fasta file with that fasta file.
Y&S workflow Wrappers for functions used in the Y&S workflow.
`transdecoder_long_orfs()`	Find long open reading frames.
`transdecoder_predict()`	Predict coding regions.
`fix_names_from_transdecoder()`	Shorten names in fasta headers.
`cd_hit_est()`	Cluster DNA sequences.
`blast_to_mcl()`	Prepare BLAST results for MCL.
`mcl()`	Run mcl.
`write_fasta_files_from_mcl()`	Write fasta files from MCL results.
`fasta_to_tree()`	Infer trees from fasta files.
`trim_tips()`	Trim tips.
`mask_tips_by_taxonID_transcripts()`	Mask tips in tree.
`cut_long_internal_branches()`	Cut long internal branches in tree.
`write_fasta_files_from_trees()`	Write fasta files from trees.
`filter_1to1_orthologs()`	Identify orthologs using the "one-to-one" method.
`prune_paralogs_MI()`	Identify orthologs using the "MI" method.
`prune_paralogs_MO()`	Identify orthologs using the "MO" method.
`prune_paralogs_RT()`	Identify orthologs using the "RT" method.
`write_ortholog_fasta_files()`	Write fasta files from ortholog trees.
`mafft_wrapper()`	Align all fasta files in a directory.
`phyutility_wrapper()`	Clean all alignments in a directory.
Intron masking Functions to mask introns in baits.
`extract_regions_from_fasta()`	Extract regions from a fasta file
`mask_regions_in_fasta()`	Mask regions in a fasta file.
`find_bed_regions()`	Find genes, exons, and introns in a gff3 file
`fill_introns()`	Fill-in introns in an alignment
Bait filtering Functions to help choose a final set of baits from the pool of candidate low copy orthologs produced by the Y&S workflow.
`calculate_alignment_stats()`	Calculate summary statistics for an alignment.
`filter_fasta()`	Filter fasta files by ingroup/outgroup status and taxonomy.
Miscellaneous
`cat_files()`	Concatenate files.
`make_dir()`	Make a directory.
`set_ys_path()`	Set the default path to Y&S scripts.
`write_fasta_files()`	Write out a list of fasta files to a directory
Example data
`onekp_data`	Taxonomic data for fern transcriptomes
`example_transcriptomes`	Fern transcriptome
Deprecated
`tcs()`	Calculate TCS.
`tcs_loop()`	tcs_loop

Reference

BLAST

Y&S workflow

Intron masking

Bait filtering

Miscellaneous

Example data

Deprecated

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