Input tree file to phylip

Question

[eng_samar_zayed]

I want to insert tree file that contain 2 trees to fitch program in PHYLIP

but , it appears error say : species name may not contain characters () : ; , [] in name in species number 1 there is a character (

And my file contain :

2 (((((alignment2,alignment3),alignment6),alignment5),alignment4),alignment7,alignment1);

(alignment7,(alignment5,((alignment2,(alignment3,alignment6)),alignment4)),alignment1);

where is my wrong ??

[Jean-Karim Heriche]

Check that fitch accepts multiple trees as input. I think it doesn't. Also check that the tree is correctly formatted. See the documentation for the options to the distance programs in PHYLIP here.

[eng_samar_zayed]

I already read that documentation but it doesn't indicate this part , i also entered file with only one tree and have the same error .

Is PHYLIP accept tree file as first input without any distance matrix ?? there is also no indiacation about that

[Jean-Karim Heriche]

Did you see this part:

U the User tree option. The trees in Fitch are regarded as unrooted, and are specified with a trifurcation (three-way split) at their base: e. g.: ((A,B),C,(D,E));

Your tree doesn't look unrooted to me.

[eng_samar_zayed]

this tree file is output from using neighbor program in PHYLIP and it said in outfile that it is unrooted tree .

and i passed it to retree program in PHYLIP and output the same file .... where is my wrong ??