# Identification and classification of duplicated genes

## Documentation for package ‘doubletrouble’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cds_scerevisiae | Coding sequences (CDS) of S. cerevisiae
classify_genes | Classify genes into unique modes of duplication
classify_gene_pairs | Classify duplicate gene pairs based on their modes of duplication
classify_ssd_pairs | Classify small-scale duplication-derived gene pairs into subcategories
diamond_inter | Interspecies DIAMOND output for yeast species
diamond_intra | Intraspecies DIAMOND output for S. cerevisiae
find_ks_peaks | Find peaks in a Ks distribution with Gaussian Mixture Models
get_anchors_list | Get a list of anchor pairs for each species
get_transposed | Get transposed duplicate pairs
get_wgd_pairs | Get gene pairs derived from whole-genome and small-scale duplications
gmax_ks | Duplicate pairs and Ks values for Glycine max
pairs2kaks | Calculate Ka, Ks, and Ka/Ks from duplicate gene pairs
plot_ks_peaks | Plot histogram of Ks distribution with peaks
scerevisiae_kaks | Duplicate pairs and Ka, Ks, and Ka/Ks values for S. cerevisiae
split_pairs_by_peak | Split gene pairs based on their Ks peaks
yeast_annot | Genome annotation of the yeast species S. cerevisiae and C. glabrata
yeast_seq | Protein sequences of the yeast species S. cerevisiae and C. glabrata