####### Compiling the list of available methods ... (will take a few seconds) ####### Methods For which an Interface is available in T-Coffee You must install the packages yourself when required (use the provided address) Contact us if you need an extra method to be added [cedric.notredame@europe.com] ****** Pairwise Sequence Alignment Methods: -------------------------------------------- fast_pair built_in [pg: t_coffee is Installed] exon3_pair built_in [pg: t_coffee is Installed] exon2_pair built_in [pg: t_coffee is Installed] exon_pair built_in [pg: t_coffee is Installed] slow_pair built_in [pg: t_coffee is Installed] proba_pair built_in [pg: t_coffee is Installed] best_pair4prot built_in [pg: t_coffee is Installed] lalign_id_pair built_in [pg: t_coffee is Installed] seq_pair built_in [pg: t_coffee is Installed] externprofile_pair built_in [pg: t_coffee is Installed] hh_pair built_in [pg: t_coffee is Installed] profile_pair built_in [pg: t_coffee is Installed] cdna_fast_pair built_in [pg: t_coffee is Installed] cdna_cfast_pair built_in [pg: t_coffee is Installed] clustalw_pair ftp://www.ebi.ac.uk/pub/clustalw [pg: clustalw is Installed] mafft_pair http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/ [pg: mafft is Installed] mafftjtt_pair http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/ [pg: mafft is Installed] mafftgins_pair http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/ [pg: mafft is Installed] dialigntx_pair http://dialign-tx.gobics.de/ [pg: dialign-tx is Installed] dialignt_pair http://dialign-t.gobics.de/ [pg: dialign-t is Installed] poa_pair http://www.bioinformatics.ucla.edu/poa/ [pg: poa is Installed] probcons_pair http://probcons.stanford.edu/ [pg: probcons is Installed] muscle_pair http://www.drive5.com/muscle/ [pg: muscle is Installed] t_coffee_pair http://www.tcoffee.org [pg: t_coffee is Installed] pcma_pair ftp://iole.swmed.edu/pub/PCMA/ [pg: pcma is Installed] kalign_pair http://msa.cgb.ki.se [pg: kalign is Installed] amap_pair http://bio.math.berkeley.edu/amap/ [pg: amap is Installed] proda_pair http://bio.math.berkeley.edu/proda/ [pg: proda is Installed] prank_pair http://www.ebi.ac.uk/goldman-srv/prank/ [pg: prank is Installed] consan_pair http://selab.janelia.org/software/consan/ [pg: sfold is Installed] ****** Pairwise Structural Alignment Methods: -------------------------------------------- align_pdbpair built_in [pg: t_coffee is Installed] lalign_pdbpair built_in [pg: t_coffee is Installed] extern_pdbpair built_in [pg: t_coffee is Installed] thread_pair built_in [pg: t_coffee is Installed] fugue_pair http://www-cryst.bioc.cam.ac.uk/fugue/download.html [pg: fugueali is Installed] pdb_pair built_in [pg: t_coffee is Installed] sap_pair http://mathbio.nimr.mrc.ac.uk/wiki/Software [pg: sap is Installed] mustang_pair http://www.cs.mu.oz.au/~arun/mustang/ [pg: mustang is Installed] TMalign_pair http://zhang.bioinformatics.ku.edu/TM-align/ [pg: TMalign is Installed] ****** Multiple Sequence Alignment Methods: -------------------------------------------- clustalw_msa ftp://www.ebi.ac.uk/pub/clustalw [pg: clustalw is Installed] mafft_msa http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/ [pg: mafft is Installed] mafftjtt_msa http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/ [pg: mafft is Installed] mafftgins_msa http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/ [pg: mafft is Installed] dialigntx_msa http://dialign-tx.gobics.de/ [pg: dialign-tx is Installed] dialignt_msa http://dialign-t.gobics.de/ [pg: dialign-t is Installed] poa_msa http://www.bioinformatics.ucla.edu/poa/ [pg: poa is Installed] probcons_msa http://probcons.stanford.edu/ [pg: probcons is Installed] muscle_msa http://www.drive5.com/muscle/ [pg: muscle is Installed] t_coffee_msa http://www.tcoffee.org [pg: t_coffee is Installed] pcma_msa ftp://iole.swmed.edu/pub/PCMA/ [pg: pcma is Installed] kalign_msa http://msa.cgb.ki.se [pg: kalign is Installed] amap_msa http://bio.math.berkeley.edu/amap/ [pg: amap is Installed] proda_msa http://bio.math.berkeley.edu/proda/ [pg: proda is Installed] prank_msa http://www.ebi.ac.uk/goldman-srv/prank/ [pg: prank is Installed] ####### Prediction Methods available to generate Templates ------------------------------------------------------------- RNAplfold http://www.tbi.univie.ac.at/~ivo/RNA/ [pg: RNAplfold is Installed] HMMtop www.enzim.hu/hmmtop/ [pg: hmmtop is Installed] GOR4 http://mig.jouy.inra.fr/logiciels/gorIV/ [pg: gorIV is Installed] wublast_client built_in [pg: wublast.pl is Installed] blastpgp_client built_in [pg: blastpgp.pl is Installed] ncbi_netblast ftp://ftp.ncbi.nih.gov/blast/executables/LATEST [pg: blastcl3 is Installed] local_ncbiblast ftp://ftp.ncbi.nih.gov/blast/executables/LATEST [pg: blastpgp is NOT Installed] All these Methods are supported by T-Coffee, but you HAVE to install them yourself [use the provided address] These methods were selected because they are freeware opensource, easy to install and well supported Contact us if you need an extra method to be added [cedric.notredame@europe.com]