Family has no SP.. species CAFE message

Question

[gu.fernandezn]

Hi i've been trying to estimate gene expansion using CAFE following the tutorial as first spet with good results, but when try with my own data i got "Family has no SP1 species" message. i have tryed differents ways to generate the tree, assuming that is the problem(ape library, ete3,Phylogeny.fr ), even use a contraction of the tree given in the tutorial(to discard distance problems in tree).

inputs matrix of gene expansion

FAMILY SP1 SP2 SP3 SP4 SP5 SP6

cluster363 7 1 2 2 2 0

ultrametric tree (same distance from branches to the root (SP5:70.71067812,(SP2:44.22386234,SP6:40.8569994,(SP3:13.87858782,(SP1:7.495331881,SP4:7.495331881):6.383255944):26.97841158):3.366862937):26.48681578);

comand used:

load -i gene_expansion_input_v3.2.tab -p 0.01 -l log.txt

tree (SP5:70.71067812,(SP2:44.22386234,SP6:40.8569994,(SP3:13.87858782,(SP1:7.495331881,SP4:7.495331881):6.383255944):26.97841158):3.366862937):26.48681578);

contracted tree(: ((((SP1:68.710687,SP2:68.710687):4.566771,SP3:73.277458):20.722542,SP4:94.0):38.738115,(SP5:36.302467,SP6:36.302467):96.435648);

I do not know what else to try. i will really appreciate any help or suggestion.

Answer 1

[Ben Fulton]

The format of your input table is slightly wrong. The sequence should be "Description ID species1 species2 species3....". You've left out the description field, so CAFE thinks FAMILY is the description and SP1 is the family ID. Just add the word NONE as the first field in each line of your file.

[gu.fernandezn]

Thanks a lot, now is working fine. My bad