# Conditional reciprocal best hits (CRBHits) in R

## Documentation for package ‘CRBHits’ version 0.0.4

- DESCRIPTION file.

## Help Pages

aa2rbh | aa2rbh
aabin2aastring | aabin2aastring
aafile2rbh | aafile2rbh
aastring2aabin | aastring2aabin
aastring2aln | aastring2aln
aln2aastring | aln2aastring
aln2dnastring | aln2dnastring
aly | aly-data
aly-data | aly-data
ath | ath-data
ath-data | ath-data
ath_aly_crbh | ath_aly_crbh-data
ath_aly_crbh-data | ath_aly_crbh-data
ath_aly_ncbi_dagchainer | ath_aly_ncbi_dagchainer-data
ath_aly_ncbi_dagchainer-data | ath_aly_ncbi_dagchainer-data
ath_aly_ncbi_kaks | ath_aly_ncbi_kaks-data
ath_aly_ncbi_kaks-data | ath_aly_ncbi_kaks-data
cds2aa | cds2aa
cds2codonaln | cds2codonaln
cds2genepos | cds2genepos
cds2kaks | cds2kaks
cds2rbh | cds2rbh
cdsfile2aafile | cdsfile2aafile
cdsfile2rbh | cdsfile2rbh
codon2number | GENETIC_CODE_TCAG
codon2numberAMBIG | codon2numberAMBIG
codon2numberTCAG | codon2numberTCAG
codonmat2pnps | codonmat2pnps
codonmat2xy | codonmat2xy
col2transparent | col2transparent
compareCodons | compareCodons
CRBHitsColors | CRBHitsColors
dnabin2dnastring | dnabin2dnastring
dnastring2aln | dnastring2aln
dnastring2codonmat | dnastring2codonmat
dnastring2dnabin | dnastring2dnabin
dnastring2kaks | dnastring2kaks
filter_alnlen | filter_alnlen
filter_eval | filter_eval
filter_pident | filter_pident
filter_qcov | filter_qcov
filter_rost1999 | filter_rost1999
filter_tcov | filter_tcov
GENETIC_CODE_TCAG | GENETIC_CODE_TCAG
gff2longest | gff2longest
globalDeletion | globalDeletion
gtf2longest | gtf2longest
hiv | hiv-data
hiv-data | hiv-data
hom_pan_ensembl_kaks | hom_pan_ensembl_kaks-data
hom_pan_ensembl_kaks-data | hom_pan_ensembl_kaks-data
isoform2longest | isoform2longest
makePostalignedSeqs | makePostalignedSeqs
make_dagchainer | make_dagchainer
make_KaKs_Calculator2 | make_KaKs_Calculator2
make_last | make_last
make_vignette | make_vignette
plot_dagchainer | plot_dagchainer
plot_kaks | plot_kaks
rbh2dagchainer | rbh2dagchainer
rbh2kaks | rbh2kaks
seqid | seqid
subString | subString
tandemdups | tandemdups
uptriidx | uptriidx