Question: PAML needs branch labels in tree
1
gravatar for miles.thorburn
3 months ago by
miles.thorburn80 wrote:

I am trying to use PAML for the first time, and it's thrown up a few errors I am struggling to fix. The manual is particularly tricky to read, but I've solved most of the other problems I've come across. I am aiming to use it to calculate dN/dS for sets of genes. I used RAxML to generate my trees in Newick format, but the error message I get after executing codeml is this:

Error: need branch labels in the tree for the model..

My tree looks like this:

(chrI_BS45_CA_R_ENSGACG00000022906:2,chrI_BS49_CA_R_ENSGACG00000022906:1,chrI_BS43_CA_R_ENSGACG00000022906:1,chrI_BS47_CA_R_ENSGACG00000022906:1,chrI_BS51_CA_R_ENSGACG00000022906:1,chrI_BS53_CA_R_ENSGACG00000022906:1):1.0;

And my control file looks like this:

seqfile = /data/12_PAML/Input/Chr1/CA_R_ENSGACG00000022906_pruned.fa
outfile = /data/12_PAML/Output/Chr1/CA_R_ENSGACG00000022906_Codeml_Output.txt
treefile = /data/12_PAML/Input/Chr1/CA_R_ENSGACG00000022906_pruned.tre

noisy = 9
verbose = 1
runmode = 0

seqtype = 1
CodonFreq = 0
model = 2
NSsites = 2
icode = 0
fix_kappa = 0 
kappa = 1
fix_omega = 0
omega = 1
cleandata = 1

I've tried looking for similar answers and Ziheng has posted about similar problems saying to look at the examples folder. In it you get a trees like this:

((1,2) #1, ((3,4), 5), (6,7) ); 
or 
((_10_H._fulgens, (((__4_H._kamtschatkana, (__1_H._rufescens,
(__2_H._sorenseni, __3_H._walallensis))) #1, (__5_H._sieboldii,
(__6_H._discus_hannai, __7_H._gigantea))), (__8_H._corrugata,
__9_H._cracherodii))), _25_H._iris, ((_17_H._pustulata,
(_24_H._t.coccinea, _23_H._t.tuberculata)), (_22_H._australis,
((_18_H._midae, ((_11_H._roei, (_12_H._scalaris, _13_H._laevigata)), 
(_14_H._cyclobates, (_15_H._rubra, _16_H._conicopora)))),
((_19_H._ovina, _21_H._varia), _20_H._diversicolor)))));

I'm struggling to see the difference. I've tried removing the floating point values and running it again, but to no avail. Any help would be very much appreciated. And thank you for your time.

newick tree paml • 201 views
ADD COMMENTlink modified 9 weeks ago • written 3 months ago by miles.thorburn80
2
gravatar for miles.thorburn
9 weeks ago by
miles.thorburn80 wrote:

Turns out this was a very simple answer. For using any of the PAML models with selection, you need to designate which branch(es) on your gene tree or phylogeny where selection differs. The notation is #1 or #n if there are n branches with different strengths of selection.

ADD COMMENTlink written 9 weeks ago by miles.thorburn80
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