GENE FAMILIES ** FILES ** tab-separated files containing the orthogroups and some additional information: - I3.0_mcl_groups.matrix_withPFAM ** EXPLANATION ** - Zostera and 13 other species - BLASTP all-vs-all, e-value 1e-3 - OrthoMCL (Markov Clustering Inflation factor 3) - standard deviation of gene counts added - all PFAM domains which are present within >=70% of the genes in the orthogroup, have been added as well. columns: 1: the name of the orthologous group = gene family ID 2 - 15: the gene counts for each species 16: ranking system 17: standard deviation of the counts in column 2 - 15 18 - 31: the gene counts for each species (turned into z-counts = normalised gene count per orthogroup) 32: PFAM domains I have provided a ranking system for some families. The first character (+ or 1) indicates the amount of genes for each species, the second character (*,1 or ?) indicates the amount of species involved. Due to the multitude of configurations, any other configuration than the ones listed below, are classified as 'na'. +* : at least one gene for each species (conserved multi-copy gene family) +1 : at least one gene for one species = species-specific gene family +? : at least one gene for all but one species = species-specific loss 1* : a single gene for each species (conserved single-copy gene family) 11 : a single gene for one species = singleton 1? : a single gene for all but one species = species-specific loss in an otherwise single-copy gene family. An '!' signs indicates that the missing (in case of a ? cluster) or the species-specific family (in case of a 1 cluster) is related to the focus species, being Zostera marina