;
; This is a test file for the kaks() function from seqinr package.
; This is an alignment of the 64 possible codons so that kaks
; values are computed for possible pairs of one-codon sequences.
;
; Only finite values should be returned. Expected values are given
; in data(kaks-torture).
;
; This file was generated with the following R script :
;
; x <- words() # The 64 codons
; aa1 <- sapply(x, function(x) translate(s2c(x)))
; aa3 <- aaa(aa1)
; names <- paste(x, aa1, aa3, sep = "-")
; sequences <- as.list(toupper(x))
; write.fasta(sequences, names, file.out = "kaks-torture.fasta")
; 
>aaa-K-Lys
AAA
>aac-N-Asn
AAC
>aag-K-Lys
AAG
>aat-N-Asn
AAT
>aca-T-Thr
ACA
>acc-T-Thr
ACC
>acg-T-Thr
ACG
>act-T-Thr
ACT
>aga-R-Arg
AGA
>agc-S-Ser
AGC
>agg-R-Arg
AGG
>agt-S-Ser
AGT
>ata-I-Ile
ATA
>atc-I-Ile
ATC
>atg-M-Met
ATG
>att-I-Ile
ATT
>caa-Q-Gln
CAA
>cac-H-His
CAC
>cag-Q-Gln
CAG
>cat-H-His
CAT
>cca-P-Pro
CCA
>ccc-P-Pro
CCC
>ccg-P-Pro
CCG
>cct-P-Pro
CCT
>cga-R-Arg
CGA
>cgc-R-Arg
CGC
>cgg-R-Arg
CGG
>cgt-R-Arg
CGT
>cta-L-Leu
CTA
>ctc-L-Leu
CTC
>ctg-L-Leu
CTG
>ctt-L-Leu
CTT
>gaa-E-Glu
GAA
>gac-D-Asp
GAC
>gag-E-Glu
GAG
>gat-D-Asp
GAT
>gca-A-Ala
GCA
>gcc-A-Ala
GCC
>gcg-A-Ala
GCG
>gct-A-Ala
GCT
>gga-G-Gly
GGA
>ggc-G-Gly
GGC
>ggg-G-Gly
GGG
>ggt-G-Gly
GGT
>gta-V-Val
GTA
>gtc-V-Val
GTC
>gtg-V-Val
GTG
>gtt-V-Val
GTT
>taa-*-Stp
TAA
>tac-Y-Tyr
TAC
>tag-*-Stp
TAG
>tat-Y-Tyr
TAT
>tca-S-Ser
TCA
>tcc-S-Ser
TCC
>tcg-S-Ser
TCG
>tct-S-Ser
TCT
>tga-*-Stp
TGA
>tgc-C-Cys
TGC
>tgg-W-Trp
TGG
>tgt-C-Cys
TGT
>tta-L-Leu
TTA
>ttc-F-Phe
TTC
>ttg-L-Leu
TTG
>ttt-F-Phe
TTT