# Identification and classification of duplicated genes

## Documentation for package ‘doubletrouble’ version 1.2.5

- 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
diamond_inter | Interspecies DIAMOND output for yeast species
diamond_intra | Intraspecies DIAMOND output for S. cerevisiae
duplicates2counts | Get a duplicate count matrix for each genome
find_ks_peaks | Find peaks in a Ks distribution with Gaussian Mixture Models
fungi_kaks | Duplicate pairs and Ka, Ks, and Ka/Ks values for fungi species
get_anchors_list | Get a list of anchor pairs for each species
get_intron_counts | Get a data frame of intron counts per gene
get_segmental | Classify gene pairs derived from segmental duplications
get_tandem_proximal | Classify gene pairs derived from tandem and proximal duplications
get_transposed | Classify gene pairs originating from transposon-derived duplications
get_transposed_classes | Classify TRD genes as derived from either DNA transposons or retrotransposons
gmax_ks | Duplicate pairs and Ks values for Glycine max
pairs2kaks | Calculate Ka, Ks, and Ka/Ks from duplicate gene pairs
plot_duplicate_freqs | Plot frequency of duplicates per mode for each species
plot_ks_distro | Plot distribution of synonymous substitution rates (Ks)
plot_ks_peaks | Plot histogram of Ks distribution with peaks
plot_rates_by_species | Plot distributions of substitution rates (Ka, Ks, or Ka/Ks) per species
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