I am searching for the following files :-
cat_silent.pl: concatenate silentfiles
changeChain.pl: change the chain id of a PDB
compose_score_silent.py: generate a silentfile from a set of PDBs
createLoop.pl: create a dummy structure from a sequence of amino acids
createTemplate.pl: create a homology model template from a FASTA file and a homologous structure
make_coords_file.py: generate .coords format from native pdb (for input to cluster_info_silent.out, see below)
molecule.exe: generate JUFO file and rename ligand atoms (with addhydrogens.inp, mdl2rosetta.inp, and pdb2mdl.inp)
pdb_fasta.pl: generate a FASTA from a PDB
pdb2tag.pl: rename a PDB or set of PDBs to their tag names (as shown in the silentfile)
reconstruct_PDB_by_index: generate PDBs from abinitio-format silentfile
renumberPDBandchains.pl: renumber the residues of a PDB sequentially, starting at 1
renumberPDBatoms.pl: renumber the atoms of a PDB sequentially, starting at 1
silentDock2pdb.pl: generate PDBs from a docking silentfile
TMalign: aligns structures based on CA-CA distances
VMD: X-Windows molecular graphics viewer
getColumn.pl: display silentfile and scorefile columns
gnuplot: graphically display data
cluster_plot.pl: generate a gnuplot input file to plot the score versus another field
histogram.pl: generate a quick histogram from STDIN data
cluster.pl: automatic clustering of an abinitio-format silentfile
cluster_info_silent.out: fully configurable silentfile clustering
cluster_pdbs.pl: cluster a set of PDBs
cluster_variation.pl: find per-residue variation within a cluster
make_color_trees.py: make a dendrogram of the clusters
make_new_plot.py: make a contacts plot
Can anybody tell me where can I find them ??
Some of these are in "BioTools", which is part of the wider 3.2 package (outside the code itself).
Some of these don't have anything to do with Rosetta; notably gnuplot and VMD, which are publically available (probably open-source) software, which you can easily find on the internet.
You should also try looking through the 2.x releases.
Let me know where you found this list and I'll try to track that author down to get them to tell me where it's supposed to be.