Man pages for joelnitta/baitfindR
Find Baits for Sequence Capture

blast_n	Run a blastn query.
blast_n_list	Run blastn on all fasta files in a folder.
blast_p	Run a blastp query.
blast_to_mcl	Prepare BLAST results for MCL.
build_blast_db	Build a BLAST database.
calculate_alignment_stats	Calculate summary statistics for an alignment.
cat_files	Concatenate files.
cd_hit_est	Cluster DNA sequences.
clean_gff	Clean up data from a gff file and convert to bed format
cut_long_internal_branches	Cut long internal branches in tree.
delete_old_output	Delete old output in a folder
example_transcriptomes	Fern transcriptome
extract_blast_hits	Extract top blast hits from multiple blast output files
extract_regions_from_fasta	Extract regions from a fasta file
fasta_to_tree	Infer trees from fasta files.
fill_introns	Fill-in introns in an alignment
filter_1to1_orthologs	Identify orthologs using the "one-to-one" method.
filter_fasta	Filter fasta files by ingroup/outgroup status and taxonomy.
find_bed_regions	Find genes, exons, and introns in a gff3 file
fix_names_from_transdecoder	Shorten names in fasta headers.
get_out_hash	Get MD5 hash of all files in a folder
mafft_wrapper	Align all fasta files in a directory.
make_dir	Make a directory.
mask_regions_in_fasta	Mask regions in a fasta file.
mask_tips_by_taxonID_transcripts	Mask tips in tree.
mcl	Run mcl.
onekp_data	Taxonomic data for fern transcriptomes
phyutility_wrapper	Clean all alignments in a directory.
pipe	Pipe operator
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.
realign_with_best_hits	Realign top blast hit of multi-fasta file with that fasta...
set_ys_path	Set the default path to Y&S scripts.
tcs	Calculate TCS.
tcs_loop	tcs_loop
transdecoder_long_orfs	Find long open reading frames.
transdecoder_predict	Predict coding regions.
trim_both_ends	Trim both ends of alignment
trim_one_end	Trim columns of exclusively "n" characters from one end of...
trim_tips	Trim tips.
write_fasta_files	Write out a list of fasta files to a directory
write_fasta_files_from_mcl	Write fasta files from MCL results.
write_fasta_files_from_trees	Write fasta files from trees.
write_ortholog_fasta_files	Write fasta files from ortholog trees.