what input tree required for "-f e" to optimize branch length

Miao Sun

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Apr 5, 2018, 4:58:31 PM4/5/18

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Hello folks,

I wan to "-f e" to optimize branch lengths for given input tree under GAMMA model, but I got error all the time :

raxmlHPC -f e -t input.tre -m GTRGAMMA -s algnment -n Out_reconciled__estBr

ERROR: Expecting ')' in tree; found: character ','

,Euphorbia_prostrata,Euphorbia_hirta)ott

Does this mean that I get branch length based on a a strictly bifurcating tree? Even this tree just provide a topology? Can I provide a genera topology (like constraint tree), and estimate branch length for those in the given topology?

please help or comment if you know anything about this subject.

Thanks!

Miao

Alexandros Stamatakis

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Apr 6, 2018, 1:00:57 AM4/6/18

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your input must be a strictly bifurcating tree in Newick format,

Alexis

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Miao Sun

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Apr 6, 2018, 9:40:59 AM4/6/18

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Thank you Alexis for confirmation! Then I don't to torture my non-bifurcating tree any more. :)

Miao

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