UsageΒΆ

Use the command backtranslate to find substitutions that explain an amino acid change:

$ backtranslate with_dna -o 210 data/mhv.fa - 1 Leu
1       A       C
1       A       T

If no reference is available, use the without_dna subcommand:

$ backtranslate without_dna - Asp 92 Tyr
274     G       T

The command find_stops finds a list of positions and substitutions that lead to stop codons. This list of destructive substitutions are useful when analysing a pool of viral transcripts. Counting the appropriate nucleotides at the given positions gives insight into how many transcripts are active.

$ backtranslate find_stops -o 210 data/mhv.fa -
216     A       T
225     A       T
230     C       A
230     C       G
243     A       T
...