Commented the lines containing pssm output.

computePred.R

@@ -38,9 +38,9 @@ aliVeryCons = ali[pId>0.8,]
 N = c(dim(ali)[[1]],dim(aliCons)[[1]],dim(aliVeryCons)[[1]])
 #resAliCons = computePSSM(aliCons)
 res = list(computePSSM(ali,N[1],npos),computePSSM(aliCons,N[2],npos),computePSSM(aliVeryCons,N[3],npos))
-write.table(res[[1]][[3]],paste0(prot,"_pssm.txt"))
-write.table(res[[2]][[3]],paste0(prot,"_pssm60.txt"))
-write.table(res[[3]][[3]],paste0(prot,"_pssm80.txt"))
+# write.table(res[[1]][[3]],paste0(prot,"_pssm.txt"))
+# write.table(res[[2]][[3]],paste0(prot,"_pssm60.txt"))
+# write.table(res[[3]][[3]],paste0(prot,"_pssm80.txt"))
 
 # read evolutionary traces computed by JET
 jet=read.table(paste(prot,"_jet.res",sep=""),head=TRUE)