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.