-- These are all vowels, but all 'a's are equivalent with respect to this
-- scoring. It is only required to give 'EqSet's if you have more than one
-- equivalent character. In this EqSet, everything gets a score of 'Eq Vowel'
-- (==2).
EqSet Vowel a å æ 4 Я я Α α ʌ а
EqSet Vowel e ê ɛ 3 Ε ε
EqSet Vowel i I y Y ɨ ʸ И и Η η Ι ι υ
EqSet Vowel o ø 0 O Ω ω
EqSet Vowel u ʏ У у Ю ю ʊ
-- These are sets of characters belonging to a certain class. In this case, we
-- have consonants.
Set Conso    c q w x 6 9 ɲ ʔ ʕ
Set Liquid   r 7 ʁ
EqSet Conso  h H ħ Х х x Χ χ
EqSet Conso  Б б B b Β β
EqSet Conso  В в V v
EqSet Conso  Г г G g Γ γ
EqSet Conso  Д д D d Δ δ ð ɣ
EqSet Conso  Ж ж ʒ č
EqSet Conso  З з z Z Ζ ζ
EqSet Conso  Й й j J
EqSet Conso  К к K k Κ κ
EqSet Liquid  Л л l L Λ λ ƛ
EqSet Conso  М м m M Μ μ
EqSet Conso  Н н N n Ν ν
EqSet Conso  П п P p Π π
EqSet Р р R r Ρ ρ
EqSet Conso  С с S s Σ σ
EqSet Conso  Т т t T Τ τ
EqSet Conso  Ф ф F f V v υ Φ φ
EqSet Conso  Ц ц
EqSet Conso  Ч ч
EqSet Conso  Ш ш ʃ š
EqSet Conso  Щ щ
EqSet Conso  Ь ь
EqSet Conso  Θ θ
EqSet Conso  Ξ ξ
EqSet Conso  Ψ ψ
-- Here we say that whenever we see a consonant aligned to the same consonant
-- in the other word, give this score.
Eq Conso   4
Eq Liquid  3
Eq Vowel   2
-- Whenever we align two consonants that are not equal (or equivalent) we give
-- this score.
InSet   Conso    Conso     0
InSet   Conso    Liquid   -1
InSet   Conso    Vowel    -999999
InSet   Liquid   Conso    -1
InSet   Liquid   Liquid   -1
InSet   Liquid   Vowel    -1
InSet   Vowel    Conso    -999999
InSet   Vowel    Liquid   -1
InSet   Vowel    Vowel     0
-- How to score a gap in a sequence
Gap         -4
-- Later on we want affine gap scoring, it's already here but not used
GapOpen     -4
GapExtend   -1
-- This score is used when we align the same character but it's one we didn't
-- specify in our sets
Match        1
-- And finally how to score a mismatch that doesn't fit into the above
Mismatch    -999999