tcoffee-deps.txt

align_pdb   ?? structure_pairwise_aligner		
amap        https://github.com/mes5k/amap-align/archive/amap.zip
blastall    ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz
blastpgp.pl http://www.ebi.ac.uk/Tools/webservices/services/blastpgp
clustalo    http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz
clustalw    http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz
clustalw2   http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz
dalilite.pl http://www.ebi.ac.uk/Tools/webservices/services/dalilite
dca         https://bibiserv2.cebitec.uni-bielefeld.de/applications/dca/resources/downloads/dca-1.1-src.tar.gz
dialign-t   http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz	
dialign-tx  http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz	
fsa         http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/
fugueali    http://mizuguchilab.org/fugue/
gorIV       http://www.tcoffee.org/Packages/mirrors/GOR_IV.tar.gz
hmmtop      http://www.tcoffee.org/Packages/mirrors/hmmtop2.1.tgz
kalign      http://msa.cgb.ki.se/downloads/kalign/current.tar.gz
legacy_blast.pl ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz
mafft       http://mafft.cbrc.jp/alignment/software/mafft-7.310-with-extensions-src.tgz
msa         ftp://ftp.ncbi.nih.gov/pub/msa/msa.tar.Z		
msaprobs    https://sourceforge.net/projects/msaprobs/files/MSAProbs-MPI/MSAProbs-MPI_rel1.0.5.tar.gz
mus4        http://www.drive5.com/muscle/muscle4.0_src.tar.gz
muscle      http://www.drive5.com/muscle/downloads3.7/muscle3.7_src.tar.gz
mustang     http://lcb.infotech.monash.edu.au/mustang/mustang_v3.2.3.tgz
pcma        http://prodata.swmed.edu/download/pub/PCMA/pcma.tar.gz
poa source  http://downloads.sourceforge.net/poamsa/poaV2.tar.gz	
prank       http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100802.tgz
probcons    http://probcons.stanford.edu/probcons_v1_12.tar.gz
probconsRNA http://probcons.stanford.edu/probconsRNA.tar.gz
proda       http://proda.stanford.edu/proda_1_0.tar.gz
retree      http://www.tcoffee.org/Packages/mirrors/source/phylip-3.66.tar.gz
RNAplfold   http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.9.tar.gz	
sap         https://github.com/jkleinj/SAP/archive/v.1.1.3.tar.gz
sfold       http://selab.janelia.org/software/consan/
SOAP::Lite  http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL	
strike      http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2
TMalign     http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f		
upp         https://github.com/smirarab/pasta/archive/upp.zip
wublast.pl  http://www.ebi.ac.uk/Tools/webservices/services/wublast	
x3dna       http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz
XML::Simple http://search.cpan.org/~grantm/XML-Simple-2.18/lib/XML/Simple.pm

Full link here.