phyml-raxml

[aoife doherty]

Hi Guys, basically my question is how do i take the output of modelgenerator (run on a nucleotide dataset) and put it into raxml.

when i run model generator on an amino acid alignment, the output (for the phyml.sh file) looks like this:

phyml test.fa 1 i 1 0 JTT 0.0 1 1.0 BIONJ y y

which then i can parse to pull out the model (JTT) and make a raxml tree with.

but then when i run model generator on a nucleotide alignment, a sample output looks like this (for the phyml.sh file):

phyml << EOF

test.fa

m

m

m

m

f

0.25

0.25

0.25

0.25

k

012345

1.6726801786629641

6.608680382949817

-2.2082519531249994E-5

2.173252709753943

11.842652668687018

w

r

c

4

a

y

r

c

4

a

y

y

EOF

other similar files look like this:

phyml <<EOF

test2.fa

m

m

m

v

y

r

c

4

a

y

y

EOF

Does anyone know how to convert this shell format into one which will just tell me the information need to input into raxml, such as model = XXX?

Thanks 

Aoife