Index of /easmith/research/perl

      Name                                       Last modified       Size  Description

[DIR] Parent Directory 27-Aug-2008 21:27 - [TXT] 3d_ali.extract.aligned2.pl 24-Feb-2008 21:12 11k [TXT] 3d_ali.extract.pl 24-Feb-2008 21:12 21k [TXT] COPYING 11-Feb-2008 18:51 34k [TXT] Makefile 09-Feb-2008 16:34 12k [TXT] Makefile.prior 09-Feb-2008 16:34 40k [TXT] add.restraints.wrapper.pl 24-Feb-2008 21:12 2k [TXT] align.all.seqs.to.chains.pl 24-Feb-2008 21:12 25k [TXT] align.atom.pdb.seqs.pl 24-Feb-2008 21:12 11k [TXT] align.caccts.1.pl 24-Feb-2008 21:12 12k [TXT] align.caccts.2.pl 24-Feb-2008 21:12 13k [TXT] align.chain.to.seqs.pl 24-Feb-2008 21:12 27k [TXT] align.clustered.pdbs.2.pl 24-Feb-2008 21:12 81k [TXT] align.clustered.pdbs.3.pl 24-Feb-2008 21:12 8k [TXT] align.clustered.pdbs.pl 24-Feb-2008 21:12 8k [TXT] align.consensus.chain.to.seqs.pl 24-Feb-2008 21:12 10k [TXT] align.lsqrms.wrapper.pl 24-Feb-2008 21:12 5k [TXT] align.nr.chain.to.seqs.pl 24-Feb-2008 21:12 18k [TXT] align.nr.partial.chain.to.seqs.pl 24-Feb-2008 21:12 8k [TXT] align.polymorphism.add.seqs.pl 24-Feb-2008 21:12 20k [TXT] align.polymorphism.pl 24-Feb-2008 21:12 290k [TXT] align.to.central.2.pl 24-Feb-2008 21:12 115k [TXT] align.to.central.3.pl 24-Feb-2008 21:12 83k [TXT] analyze.align.clustered.pdbs.10.pl 24-Feb-2008 21:12 34k [TXT] analyze.align.clustered.pdbs.11.pl 24-Feb-2008 21:12 19k [TXT] analyze.align.clustered.pdbs.2.pl 24-Feb-2008 21:12 9k [TXT] analyze.align.clustered.pdbs.3.pl 24-Feb-2008 21:12 11k [TXT] analyze.align.clustered.pdbs.4.pl 24-Feb-2008 21:12 14k [TXT] analyze.align.clustered.pdbs.5.pl 24-Feb-2008 21:12 14k [TXT] analyze.align.clustered.pdbs.6.pl 24-Feb-2008 21:12 13k [TXT] analyze.align.clustered.pdbs.9.pl 24-Feb-2008 21:12 10k [TXT] analyze.align.to.central.1.pl 24-Feb-2008 21:12 20k [TXT] analyze.align.to.central.2.pl 24-Feb-2008 21:12 24k [TXT] average.hetatm.4.pl 24-Feb-2008 21:12 11k [TXT] caccts.2.pl 24-Feb-2008 21:12 31k [TXT] caccts.3.pl 24-Feb-2008 21:12 42k [TXT] check.atom.distances4.pl 24-Feb-2008 21:12 5k [TXT] check.atom.distances5.pl 24-Feb-2008 21:12 4k [TXT] check.for.bumps.2.pl 24-Feb-2008 21:12 5k [TXT] check.main.chain.distances.2.pl 24-Feb-2008 21:12 4k [TXT] check.pdb.vs.pfam.pl 24-Feb-2008 21:12 488k [TXT] check.side.chain.distances.1.pl 24-Feb-2008 21:12 4k [TXT] check.single.structural.align.pl 24-Feb-2008 21:12 21k [TXT] check.water.for.pos.ions.pl 24-Feb-2008 21:12 7k [TXT] cluster.chain.to.seq.pl 24-Feb-2008 21:12 34k [TXT] combine.align.to.central.3.pl 24-Feb-2008 21:12 67k [TXT] combine.nr.uniref3.pl 19-Mar-2008 17:34 25k [TXT] combine.structural.align.groups.pl 24-Feb-2008 21:12 279k [TXT] compare.trees.problems.pl 24-Feb-2008 21:12 27k [TXT] consensus.2.chain.to.seqs.pl 24-Feb-2008 21:12 8k [TXT] consensus.2.nr.chain.to.seqs.pl 24-Feb-2008 21:12 10k [TXT] consensus.align.consensus.chain.to.seqs.pl 24-Feb-2008 21:12 30k [TXT] consensus.chain.to.seqs.pl 24-Feb-2008 21:12 7k [TXT] consensus.nr.chain.to.seqs.pl 24-Feb-2008 21:12 13k [TXT] consensus4.multiple.pl 24-Feb-2008 21:12 21k [TXT] consensus5.multiple.pl 24-Feb-2008 21:12 22k [TXT] convert.structal.pl 24-Feb-2008 21:12 71k [TXT] create.freezegrps.2.pl 24-Feb-2008 21:12 11k [TXT] create.ins.del.mutate.freezegrps.2.pl 24-Feb-2008 21:12 32k [TXT] create.mkrotscr.mutate.1.loop.pl 24-Feb-2008 21:12 23k [TXT] create.mkrotscr.mutate.2.loop.pl 24-Feb-2008 21:14 7k [TXT] create.outgroup.seqs.pl 24-Feb-2008 21:12 54k [TXT] create.restraints.1.pl 24-Feb-2008 21:12 10k [TXT] create.restraints.2.pl 24-Feb-2008 21:12 15k [TXT] create.similarity.matrix.1.pl 24-Feb-2008 21:12 17k [TXT] create.tree.section.pl 24-Feb-2008 21:12 17k [TXT] determine.parsimony.species.pl 24-Feb-2008 21:12 40k [TXT] do.reduce3.restore.pl 24-Feb-2008 21:12 3k [TXT] estimate.starting.dists.3.pl 24-Feb-2008 21:12 247k [TXT] extract.30.pairs.pl 24-Feb-2008 21:12 23k [TXT] extract.atom.seqs.pl 24-Feb-2008 21:12 53k [TXT] extract.chain.records.pl 24-Feb-2008 21:12 6k [TXT] extract.important.pdbs.pl 24-Feb-2008 21:12 43k [TXT] extract.needed.pdbs.for.loop.search.pl 24-Feb-2008 21:12 3k [TXT] extract.protein.clusters.pl 24-Feb-2008 21:12 121k [TXT] extract.r.values.pl 24-Feb-2008 21:12 19k [TXT] extract.species.names.pl 24-Feb-2008 21:12 511k [TXT] extract.sptrembl.polymorphism.pl 24-Feb-2008 21:12 28k [TXT] figure.out.kingdom.norm.dists.pl 24-Feb-2008 21:12 5k [TXT] find.AO.NO.AOP.constraints.2.pl 24-Feb-2008 21:12 28k [TXT] find.align.thresholds.pl 24-Feb-2008 21:12 23k [TXT] find.distance.deviations.2.pl 24-Feb-2008 21:12 70k [TXT] find.distance.min.max.matrices.pl 24-Feb-2008 21:14 37k [TXT] find.helix.coil.sub.groups.pl 24-Feb-2008 21:12 16k [TXT] find.interacting.res.pl 24-Feb-2008 21:14 23k [TXT] find.pdbatom.stockholm.alignment.pl 24-Feb-2008 21:12 39k [TXT] find.residue.correlations.2.pl 24-Feb-2008 21:14 37k [TXT] find.residue.correlations.pl 24-Feb-2008 21:14 37k [TXT] find.species.weights.2.pl 24-Feb-2008 21:12 39k [TXT] find.species.weights.3.pl 24-Feb-2008 21:12 38k [TXT] find.sub.groups.pl 24-Feb-2008 21:12 13k [TXT] group.to.msf.pl 24-Feb-2008 21:12 54k [TXT] group.to.msf.spread.pl 24-Feb-2008 21:12 27k [TXT] homstrad.extract.pl 24-Feb-2008 21:12 26k [TXT] integrate.sequence.align.1.pl 24-Feb-2008 21:12 230k [TXT] integrate.structural.align.1.pl 24-Feb-2008 21:12 459k [TXT] integrate.structural.align.2.pl 24-Feb-2008 21:12 290k [TXT] interpret.align.pdbs.pl 24-Feb-2008 21:12 7k [TXT] interpret.important.pdbs.pl 24-Feb-2008 21:12 99k [TXT] interpret.pdb.clusters.pl 24-Feb-2008 21:12 67k [TXT] interpret.probe.pl 24-Feb-2008 21:12 9k [TXT] interpret.protein.files.pl 24-Feb-2008 21:12 311k [TXT] interpret.ring.changes.pl 24-Feb-2008 21:12 19k [TXT] list.polymorphism.pl 24-Feb-2008 21:12 20k [TXT] nexus.add.freqs.pl 24-Feb-2008 21:12 207k [TXT] nexus.add.gap.partitions.pl 24-Feb-2008 21:12 44k [TXT] nexus.add.groups.2.pl 24-Feb-2008 22:35 53k [TXT] nexus.add.kingdom.constraints.pl 24-Feb-2008 21:12 39k [TXT] nexus.add.usertree.section.pl 24-Feb-2008 21:12 37k [TXT] nexus.add.wag.pl 24-Feb-2008 21:12 13k [TXT] nexus.cleanup.quartets.pl 24-Feb-2008 21:12 48k [TXT] nexus.consolidate.partitions.pl 24-Feb-2008 21:12 73k [TXT] nexus.create.ncbi.subtrees.10.pl 24-Feb-2008 21:12 14k [TXT] nexus.create.ncbi.subtrees.2.pl 24-Feb-2008 21:12 51k [TXT] nexus.create.ncbi.subtrees.3.pl 24-Feb-2008 21:12 15k [TXT] nexus.create.ncbi.subtrees.4.pl 24-Feb-2008 21:12 14k [TXT] nexus.create.ncbi.subtrees.5.pl 24-Feb-2008 21:12 14k [TXT] nexus.create.ncbi.subtrees.6.pl 24-Feb-2008 21:12 14k [TXT] nexus.create.ncbi.subtrees.7.pl 24-Feb-2008 21:12 14k [TXT] nexus.create.ncbi.subtrees.8.pl 24-Feb-2008 21:12 14k [TXT] nexus.create.ncbi.subtrees.9.pl 24-Feb-2008 21:12 15k [TXT] nexus.create.ncbi.subtrees.MyTree0001.pl 24-Feb-2008 21:12 19k [TXT] nexus.create.ncbi.subtrees.pl 24-Feb-2008 21:12 20k [TXT] nexus.create.ncbi.tree.pl 24-Feb-2008 21:12 55k [TXT] nexus.extract.ancestral.seq.pos.pl 24-Feb-2008 21:12 11k [TXT] nexus.extract.ancestral.seqs.2.pl 24-Feb-2008 21:12 90k [TXT] nexus.extract.ancestral.seqs.3.pl 24-Feb-2008 21:12 100k [TXT] nexus.find.init.quartets.pl 24-Feb-2008 21:12 15k [TXT] nexus.find.overall.quartets.1.pl 24-Feb-2008 21:12 57k [TXT] nexus.get.quartets.2.pl 24-Feb-2008 21:12 742k [TXT] nexus.get.quartets.2.wrapper.pl 24-Feb-2008 21:12 2k [TXT] nexus.get.quartets.kingdom.pl 24-Feb-2008 21:12 257k [TXT] nexus.get.quartets.pl 24-Feb-2008 21:12 249k [TXT] nexus.get.quartets.recover.pl 24-Feb-2008 21:12 250k [TXT] nexus.get.quartets.recover2.pl 24-Feb-2008 21:12 252k [TXT] nexus.get.quartets.recover3.pl 24-Feb-2008 21:12 252k [TXT] nexus.interpret.treebase.trees.pl 24-Feb-2008 21:12 251k [TXT] nexus.make.charset.seqs.pl 24-Feb-2008 21:12 17k [TXT] nexus.remove.excluded.pl 24-Feb-2008 21:12 16k [TXT] nexus.simplify.full.species.2.pl 24-Feb-2008 21:12 27k [TXT] nexus.simplify.full.species.pl 24-Feb-2008 21:12 36k [TXT] nexus.simplify.polymorphism.pl 24-Feb-2008 21:12 26k [TXT] nexus.split.non_metazoa.quartets.pl 24-Feb-2008 21:12 18k [TXT] nexus.use.recdcm3.subsets.pl 24-Feb-2008 21:12 238k [TXT] pdb.get.chains.pl 24-Feb-2008 21:12 9k [TXT] pdb.nr.embl.swissprot.pl 24-Feb-2008 21:12 10k [TXT] pdb.nr.multiple.pl 24-Feb-2008 21:12 19k [TXT] pdb.nr.multiple2.pl 24-Feb-2008 21:12 32k [TXT] pdb.replaced.groups.pl 24-Feb-2008 21:12 8k [TXT] pdb.species.extract.pl 24-Feb-2008 21:12 19k [TXT] pdbeast.species.extract2.pl 24-Feb-2008 21:12 139k [TXT] pfam.swissprot.to.pdb.pl 24-Feb-2008 21:12 60k [TXT] process.align.to.central.pl 24-Feb-2008 21:12 37k [TXT] process.structural.align.pl 24-Feb-2008 21:12 58k [TXT] process2.structural.align.pl 24-Feb-2008 21:12 39k [TXT] protein.replaced.groups2.pl 24-Feb-2008 21:12 54k [TXT] put.dists.on.tree.pl 24-Feb-2008 21:12 20k [TXT] put.together.pdbs.section.3.pl 24-Feb-2008 21:12 177k [TXT] put.together.pdbs.section.4.pl 24-Feb-2008 21:12 180k [TXT] put.together.pdbs.sequence.3.pl 24-Feb-2008 21:13 111k [TXT] quartets.to.weights.pl 24-Feb-2008 21:12 4k [TXT] quartets.to.wr.modified.pl 24-Feb-2008 21:12 8k [TXT] recdcm3.get.subsets.pl 24-Feb-2008 21:12 729k [TXT] reformat.gromacs.pdb.pl 24-Feb-2008 21:12 9k [TXT] reformat.pdb.gromacs.pl 24-Feb-2008 21:12 12k [TXT] restore.reduce3.removed.pl 24-Feb-2008 21:13 8k [TXT] ring.changes.lsqrms.pl 24-Feb-2008 21:12 52k [TXT] rotrans.lsqrms.pl 24-Feb-2008 21:12 5k [TXT] run.lsqrms.pl 24-Feb-2008 21:12 27k [TXT] select.aligned.important.pdbs.pl 24-Feb-2008 21:12 96k [TXT] split.showalign.html.pl 24-Feb-2008 21:12 4k [TXT] sprot.group.protein.files.pl 24-Feb-2008 21:12 36k [TXT] sprot.pdb.DR.extract2.pl 24-Feb-2008 21:12 77k [TXT] sprot.pdb.species.extract.pl 24-Feb-2008 21:12 93k [TXT] summarize.chain.lengths.pl 24-Feb-2008 21:12 41k [TXT] sump.summarize.pl 24-Feb-2008 21:12 4k [TXT] sump.summarize2.pl 24-Feb-2008 21:12 4k [TXT] swissprot.scop.species2.pl 24-Feb-2008 21:12 117k [TXT] swissprot.species3.filter3.pl 24-Feb-2008 21:12 101k [TXT] test.find.quartets.1.pl 24-Feb-2008 21:12 100k [TXT] to.gromacs.wrapper.2.pl 24-Feb-2008 21:12 5k [TXT] transfer.weights.to.stockholm.1.pl 24-Feb-2008 21:12 16k [TXT] tree.simplify.full.pl 24-Feb-2008 21:12 6k [TXT] uniref.to.nr.pl 19-Mar-2008 17:34 2k [TXT] use.mrbayes.sump.freqs.info.2.pl 24-Feb-2008 21:12 17k [TXT] use.mrbayes.sump.freqs.info.pl 24-Feb-2008 21:12 10k

All software in this directory is copyrighted 2001-2008 by Allen Watkins Smith.
It is available under the GNU Affero General Public License, version 3.0 or
later, at your option; see the file COPYING for version 3.0, or
http://www.gnu.org/licenses/ for later versions.