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PaSSml --> Phylogeny and Secondary Structure using ML

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this program infers branch lengths of an evolutionary tree from a multialignment of amino acid sequences and predicts or improves secondary structure

- job file name: passml.inp (ASCII format)

- verbose file name: prolix (all the trees evaluated)

PARAMETERS:

a) secondary structure y/n:

b) accessibility y/n:

c) number sequences :

d) protein length :

e) user tree y/n:

f) use branch lengths y/n:

g) sequence filename (a short one):

h) sequential or aligned s/i:

i) output file (a short one):

j) eigen file: eigen

k) model file: rhoij38

l) aa stationary probabilities file: rev38

m) HMM (a), HMM &1st category is Coil exposed (b) [NULL model (c)]:

n) structure prediction: No (a), H(helix)_E(sheet)_O(others) (b), H_E_T(turn)_O (c), b(buried)_e(exposed) (d), H_E_T_O * b_e (e):

o) [ancestral node prediction]: n

p) [bootstrap analysis] y/n: n

q) quit y/n: n

choose a letter (. to accept) :>