Upvoting, plus some additional thoughts.
You have a tree, and you're interested in support values from a distribution of trees you've already generated (regardless of approach). You want to make a consensus tree (perhaps majority-rule to account for any uncertainty in your point estimate?), and you can get nodal support values (frequentist or Bayesian) from these trees using any of the approaches outlined in this answer. I don't know how you bootstrapped or jackknifed without an alignment - how did you model your sequence evolution?
You have a few other questions and pieces of information:
I am not using the traditional sequence concatination and then MSA then constructing a Tree, that's why.
Concatenation assumes a single evolutionary history and model of sequence evolution applies across your alignment. There are established approaches for accounting for discordance among loci when inferring trees that have been developed over the past decade or so. You may consider searching the literature for "how to estimate species trees."
I have a pylogenetic tree for over 3,000 prokaryotic genomes. I have made many replicates of this tree using jacknife approach. So now I have many variants of this tree
Estimating trees from datasets this size can be hard, especially if you don't have the alignment. RAxML can handle large datasets and also perform bootstrapping. But, how are you even arriving at these sets of trees? What software? Are you dropping tips from your source tree and looking at, say, triplets or quartets? I don't understand and can't really provide guidance until I do.
I'm aware that there are many variables in my question, first of all how would I define a clade? ...
A clade is, by definition, a monophyletic group. Delimiting prokaryotic species is beyond the scope of this phylogenetic question. You may consider calculating a variety of tree distances (Robinson-Foulds, Kuhner-Felsenstein) to calculate discordance among sets of trees. Perhaps start here.
What software did you use to create the jackknife-ed trees? PAUP* can perform jackknife replicates and provide a consensus tree. See page 77 of the manual http://www.phylo.org/sub_sections/PAUP_Cmd_ref_v2.pdf
and a tut here: http://ib.berkeley.edu/courses/ib200a/labs/ib200a_lab10_bootstrap_jackknife_bremer.pdf
Thank you for your reply Amar, I made my own jackknifed trees because I am proposing my own way of constructing a phylogenetic tree, so I have allready a list of tree variations (I am not using the traditional sequence concatination and then MSA then constructing a Tree, that's why)
so I was looking into PAUP, I'm not sure if this is going to work, it seems like it takes sequence alignment as input and then starts removing alignment columns etc. I have the tree allready and will take it from there, like I said I can also make my jackknifed trees, so the problem is more like given a set of jackknifed trees is there a program that will give me statistics about certain monophyletic clades and their relative frequencies in all the smaller variations of trees?