    ## Use a real coding sequence:
    rcds <- read.fasta("virus.fasta")
    uco( rcds, index = "freq")
    uco( rcds, index = "eff")
    uco( rcds, index = "rscu")
    uco( rcds, as.data.frame = TRUE)

Guys, anyone to help me. I used those functions as directed in uco(seqinr) package for relative synonymous codon usage (rscu) computaion the results were as shown below. The fasta file has multiple fasta sequences. What is wrong?



    aaa aac aag aat aca acc acg act aga agc agg agt 
      0   0   0   0   0   0   0   0   0   0   0   0 
    ata atc atg att caa cac cag cat cca ccc ccg cct 
      0   0   0   0   0   0   0   0   0   0   0   0 
    cga cgc cgg cgt cta ctc ctg ctt gaa gac gag gat 
      0   0   0   0   0   0   0   0   0   0   0   0 
    gca gcc gcg gct gga ggc ggg ggt gta gtc gtg gtt 
      0   0   0   0   0   0   0   0   0   0   0   0 
    taa tac tag tat tca tcc tcg tct tga tgc tgg tgt 
      0   0   0   0   0   0   0   0   0   0   0   0 
    tta ttc ttg ttt 
      0   0   0   0 
    > uco( rcds, index = "eff")
    
    aaa aac aag aat aca acc acg act aga agc agg agt 
      0   0   0   0   0   0   0   0   0   0   0   0 
    ata atc atg att caa cac cag cat cca ccc ccg cct 
      0   0   0   0   0   0   0   0   0   0   0   0 
    cga cgc cgg cgt cta ctc ctg ctt gaa gac gag gat 
      0   0   0   0   0   0   0   0   0   0   0   0 
    gca gcc gcg gct gga ggc ggg ggt gta gtc gtg gtt 
      0   0   0   0   0   0   0   0   0   0   0   0 
    taa tac tag tat tca tcc tcg tct tga tgc tgg tgt 
      0   0   0   0   0   0   0   0   0   0   0   0 
    tta ttc ttg ttt 
      0   0   0   0 
    > uco( rcds, index = "rscu")
    aaa aac aag aat aca acc acg act aga agc agg agt 
     NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
    ata atc atg att caa cac cag cat cca ccc ccg cct 
     NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
    cga cgc cgg cgt cta ctc ctg ctt gaa gac gag gat 
     NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
    gca gcc gcg gct gga ggc ggg ggt gta gtc gtg gtt 
     NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
    taa tac tag tat tca tcc tcg tct tga tgc tgg tgt 
     NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
    tta ttc ttg ttt 
     NA  NA  NA  NA 
    > uco( rcds, as.data.frame = TRUE)
         AA codon eff freq RSCU
    aaa Lys   aaa   0    0   NA
    aac Asn   aac   0    0   NA
    aag Lys   aag   0    0   NA
    aat Asn   aat   0    0   NA
    aca Thr   aca   0    0   NA
    acc Thr   acc   0    0   NA
    acg Thr   acg   0    0   NA
    act Thr   act   0    0   NA
    aga Arg   aga   0    0   NA
    agc Ser   agc   0    0   NA
    agg Arg   agg   0    0   NA
    agt Ser   agt   0    0   NA
    ata Ile   ata   0    0   NA
    atc Ile   atc   0    0   NA
    atg Met   atg   0    0   NA
    att Ile   att   0    0   NA
    caa Gln   caa   0    0   NA
    cac His   cac   0    0   NA
    cag Gln   cag   0    0   NA
    cat His   cat   0    0   NA
    cca Pro   cca   0    0   NA
    ccc Pro   ccc   0    0   NA
    ccg Pro   ccg   0    0   NA
    cct Pro   cct   0    0   NA
    cga Arg   cga   0    0   NA
    cgc Arg   cgc   0    0   NA
    cgg Arg   cgg   0    0   NA
    cgt Arg   cgt   0    0   NA
    cta Leu   cta   0    0   NA
    ctc Leu   ctc   0    0   NA
    ctg Leu   ctg   0    0   NA
    ctt Leu   ctt   0    0   NA
    gaa Glu   gaa   0    0   NA
    gac Asp   gac   0    0   NA
    gag Glu   gag   0    0   NA
    gat Asp   gat   0    0   NA
    gca Ala   gca   0    0   NA
    gcc Ala   gcc   0    0   NA
    gcg Ala   gcg   0    0   NA
    gct Ala   gct   0    0   NA
    gga Gly   gga   0    0   NA
    ggc Gly   ggc   0    0   NA
    ggg Gly   ggg   0    0   NA
    ggt Gly   ggt   0    0   NA
    gta Val   gta   0    0   NA
    gtc Val   gtc   0    0   NA
    gtg Val   gtg   0    0   NA
    gtt Val   gtt   0    0   NA
    taa Stp   taa   0    0   NA
    tac Tyr   tac   0    0   NA
    tag Stp   tag   0    0   NA
    tat Tyr   tat   0    0   NA
    tca Ser   tca   0    0   NA
    tcc Ser   tcc   0    0   NA
    tcg Ser   tcg   0    0   NA
    tct Ser   tct   0    0   NA
    tga Stp   tga   0    0   NA
    tgc Cys   tgc   0    0   NA
    tgg Trp   tgg   0    0   NA
    tgt Cys   tgt   0    0   NA
    tta Leu   tta   0    0   NA
    ttc Phe   ttc   0    0   NA
    ttg Leu   ttg   0    0   NA
    ttt Phe   ttt   0    0   NA
    > 
    ## Finally have resolved that problem using arrangement of the following functions:
    
    ## Use a real coding sequence:
    rcds <- read.fasta("virus.fasta")[[1]]
    uco( rcds, index = "freq")
    uco( rcds, index = "eff")
    uco( rcds, index = "rscu")
    uco( rcds, as.data.frame = TRUE, NA.rscu = NA)
    
##The output dataframe is as indicated below:
    
    > uco( rcds, as.data.frame = TRUE, NA.rscu = NA)
         AA codon eff        freq      RSCU
    aaa Lys   aaa  16 0.068669528 1.8823529
    aac Asn   aac   6 0.025751073 0.9230769
    aag Lys   aag   1 0.004291845 0.1176471
    aat Asn   aat   7 0.030042918 1.0769231
    aca Thr   aca   7 0.030042918 1.8666667
    acc Thr   acc   3 0.012875536 0.8000000
    acg Thr   acg   2 0.008583691 0.5333333
    act Thr   act   3 0.012875536 0.8000000
    aga Arg   aga   8 0.034334764 3.6923077
    agc Ser   agc   0 0.000000000 0.0000000
    agg Arg   agg   2 0.008583691 0.9230769
    agt Ser   agt   6 0.025751073 2.5714286
    ata Ile   ata   6 0.025751073 1.0588235
    atc Ile   atc   3 0.012875536 0.5294118
    atg Met   atg   4 0.017167382 1.0000000
    att Ile   att   8 0.034334764 1.4117647
    caa Gln   caa   4 0.017167382 1.3333333
    cac His   cac   2 0.008583691 1.3333333
    cag Gln   cag   2 0.008583691 0.6666667
    cat His   cat   1 0.004291845 0.6666667
    cca Pro   cca   4 0.017167382 2.0000000
    ccc Pro   ccc   1 0.004291845 0.5000000
    ccg Pro   ccg   1 0.004291845 0.5000000
    cct Pro   cct   2 0.008583691 1.0000000
    cga Arg   cga   2 0.008583691 0.9230769
    cgc Arg   cgc   0 0.000000000 0.0000000
    cgg Arg   cgg   0 0.000000000 0.0000000
    cgt Arg   cgt   1 0.004291845 0.4615385
    cta Leu   cta   1 0.004291845 0.2857143
    ctc Leu   ctc   3 0.012875536 0.8571429
    ctg Leu   ctg   3 0.012875536 0.8571429
    ctt Leu   ctt   2 0.008583691 0.5714286
    gaa Glu   gaa   2 0.008583691 0.5714286
    gac Asp   gac   1 0.004291845 0.5000000
    gag Glu   gag   5 0.021459227 1.4285714
    gat Asp   gat   3 0.012875536 1.5000000
    gca Ala   gca   5 0.021459227 2.5000000
    gcc Ala   gcc   1 0.004291845 0.5000000
    gcg Ala   gcg   0 0.000000000 0.0000000
    gct Ala   gct   2 0.008583691 1.0000000
    gga Gly   gga   4 0.017167382 2.0000000
    ggc Gly   ggc   0 0.000000000 0.0000000
    ggg Gly   ggg   1 0.004291845 0.5000000
    ggt Gly   ggt   3 0.012875536 1.5000000
    gta Val   gta   2 0.008583691 1.1428571
    gtc Val   gtc   0 0.000000000 0.0000000
    gtg Val   gtg   2 0.008583691 1.1428571
    gtt Val   gtt   3 0.012875536 1.7142857
    taa Stp   taa  11 0.047210300 1.2222222
    tac Tyr   tac   4 0.017167382 0.5333333
    tag Stp   tag   8 0.034334764 0.8888889
    tat Tyr   tat  11 0.047210300 1.4666667
    tca Ser   tca   2 0.008583691 0.8571429
    tcc Ser   tcc   4 0.017167382 1.7142857
    tcg Ser   tcg   1 0.004291845 0.4285714
    tct Ser   tct   1 0.004291845 0.4285714
    tga Stp   tga   8 0.034334764 0.8888889
    tgc Cys   tgc   4 0.017167382 1.1428571
    tgg Trp   tgg   6 0.025751073 1.0000000
    tgt Cys   tgt   3 0.012875536 0.8571429
    tta Leu   tta   4 0.017167382 1.1428571
    ttc Phe   ttc   4 0.017167382 0.6153846
    ttg Leu   ttg   8 0.034334764 2.2857143
    ttt Phe   ttt   9 0.038626609 1.3846154
    > 
Thank you again in advance!