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Searched refs:outgroup (Results 1 – 25 of 122) sorted by relevance

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/dports/net/mpich2/mpich2-1.5/test/mpi/group/
H A Dgroupnullincl.c16 MPI_Group group, outgroup; in main() local
28 rc = MPI_Group_incl( group, 0, 0, &outgroup ); in main()
35 rc = MPI_Group_incl( group, 0, ranks, &outgroup ); in main()
43 if (outgroup != MPI_GROUP_EMPTY) { in main()
45 rc = MPI_Group_compare( outgroup, MPI_GROUP_EMPTY, &result ); in main()
57 if (outgroup != MPI_GROUP_NULL) { in main()
58 rc = MPI_Group_free( &outgroup ); in main()
/dports/net/mpich/mpich-3.4.3/test/mpi/group/
H A Dgroupnullincl.c15 MPI_Group group, outgroup; in main() local
28 rc = MPI_Group_incl(group, 0, 0, &outgroup); in main()
35 rc = MPI_Group_incl(group, 0, ranks, &outgroup); in main()
43 if (outgroup != MPI_GROUP_EMPTY) { in main()
45 rc = MPI_Group_compare(outgroup, MPI_GROUP_EMPTY, &result); in main()
57 if (outgroup != MPI_GROUP_NULL) { in main()
58 rc = MPI_Group_free(&outgroup); in main()
/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/
H A Dete_mod.py109 if args.outgroup and args.unroot:
111 elif args.outgroup:
112 if len(args.outgroup) > 1:
113 outgroup = t.get_common_ancestor(args.outgroup)
115 outgroup = t & args.outgroup[0]
116 t.set_outgroup(outgroup)
/dports/math/octave-forge-control/control-3.3.1/inst/
H A D__tito_dim__.m27 outgroup = P.outgroup; variable
30 if (! isfield (outgroup, "V"))
31 error ("%s: missing outgroup 'V'", name);
38 nmeas = numel (outgroup.V);
44 if (! isequal (outgroup.V(:), (p-nmeas+1:p)(:)))
45 error ("%s: outgroup 'V' invalid", name);
/dports/biology/checkm/CheckM-1.0.18/scripts/genometreeworkflow/
H A DrerootTree.py64 outgroup = []
76 outgroup.append(t.taxon.label)
78 … if outgroup == [] or len(outgroup) == len(taxa) or not self.__isMonophyletic(tree, outgroup):
83 mrca = tree.mrca(taxon_labels=outgroup)
/dports/biology/p5-Bio-NEXUS/Bio-NEXUS-0.78/lib/Bio/NEXUS/
H A DTree.pm686 my $outgroup = $tree->find($outgroup_name);
692 && $dist_back_to_newroot == $outgroup->get_length() )
694 $newroot = $outgroup->get_parent();
695 $outgroup->set_length($dist_back_to_newroot);
701 my $outgroup_old_parent = $outgroup->get_parent();
704 my $newroot_siblings = $outgroup->get_siblings();
710 $newroot->adopt( $outgroup, 1 );
754 my ( $outgroup, $newroot, $dist_back_to_newroot ) = @_;
755 if ( $outgroup->get_length() ) {
756 my $outgroup_length = $outgroup->get_length();
[all …]
H A DTreesBlock.pm378 my ( $self, $outgroup, $root_position, $treename ) = @_;
379 if ( not defined $treename and not defined $outgroup ) {
389 push @rerooted_trees, $tree->reroot( $outgroup, $root_position );
407 my ( $self, $outgroup, $root_position ) = @_;
411 push @rerooted_trees, $tree->reroot( $outgroup, $root_position );
/dports/math/octave-forge-control/control-3.3.1/inst/@lti/
H A D__lti_prune__.m37 …tmp = cellfun (@(x) __str2idx__ (lti.outgroup, lti.outname, x, "out"), out_idx, "uniformoutput", f…
45 if (numfields (lti.outgroup))
47 …[lti.outgroup, empty] = structfun (@(x) __group_prune__ (x, out_idx, p), lti.outgroup, "uniformout…
49 fields = fieldnames (lti.outgroup);
50 lti.outgroup = rmfield (lti.outgroup, fields(empty));
H A D__lti_group__.m47 if (numfields (lti1.outgroup) || numfields (lti2.outgroup))
49 lti2_outgroup = structfun (@(x) x + p1, lti2.outgroup, "uniformoutput", false);
50 retlti.outgroup = __merge_struct__ (lti1.outgroup, lti2_outgroup);
54 ## retlti.outgroup remains empty struct
/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/t/
H A DProtPars.t14 my @params = ('threshold'=>10,'jumble'=>'17,10',outgroup=>2,'idlength'=>10);
30 my $outgroup = 3;
31 $tree_factory->outgroup($outgroup);
33 my $new_outgroup= $tree_factory->outgroup();
72 @params = ('threshold'=>10,'jumble'=>'7,5',outgroup=>2,'idlength'=>10);
H A DNeighbor.t16 # 'outgroup'=>2,
34 my $outgroup= 1;
35 $tree_factory->outgroup($outgroup);
36 my $new_outgroup = $tree_factory->outgroup();
86 $tree_factory->outgroup('ENSP000003');
100 $tree_factory->outgroup(undef);
/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/task/
H A Dmerger.py114 outgroup = partition_pairs[0][3]
115 ttree.set_outgroup(outgroup)
139 outgroup = ttree.get_common_ancestor(out_seqs)
140 if set(outgroup.get_leaf_names()) ^ out_seqs:
145 outgroup = ttree & list(out_seqs)[0]
147 ttree.set_outgroup(outgroup)
149 found_target = outgroup.get_sisters()[0]
152 outgroup.detach()
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/TreeIO/
H A Dlintree.pm214 my ($outgroup) = $treenodes[$data{'outgroup'}->[0]];
215 if( ! defined $outgroup) {
218 $T->reroot($outgroup->ancestor);
/dports/biology/p5-Bio-Phylo/Bio-Phylo-v2.0.1/t/
H A D21-bioperl-tree.t65 '-outgroup' => $n4
83 '-outgroup' => $iADHX
100 '-outgroup' => $d
108 '-outgroup' => $d
124 '-outgroup' => $d
132 '-outgroup' => $f
142 '-outgroup' => $d
145 'A,B,C are not Monophyletic w D as outgroup'
150 '-outgroup' => $i
153 'A,F,E are monophyletic with I as outgroup'
[all …]
/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SeqIO/
H A Dmsout.t175 my $outgroup = $msout->outgroup;
176 is( $outgroup, 1, "Testing msout::outgroup" );
350 my $outgroup = $msout->outgroup;
351 is( $outgroup, 0, "Testing msout::outgroup" );
/dports/biology/py-biopython/biopython-1.79/Bio/Phylo/
H A DBaseTree.py844 outgroup = self.common_ancestor(outgroup_targets, *more_targets)
845 outgroup_path = self.get_path(outgroup)
850 prev_blen = outgroup.branch_length or 0.0
852 if outgroup.is_terminal() or outgroup_branch_length is not None:
854 outgroup.branch_length = outgroup_branch_length or 0.0
856 branch_length=self.root.branch_length, clades=[outgroup]
867 parent.clades.pop(parent.clades.index(outgroup))
870 prev_blen - outgroup.branch_length,
876 new_root = outgroup
891 if outgroup in old_root.clades:
[all …]
/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Tree/
H A DTree.t64 -outgroup => $n4),1,'Test Monophyly');
77 -outgroup=> $iADHX),1, 'non-monophyletic group');
96 -outgroup => $d),1, 'B,C are Monophyletic');
99 -outgroup => $d),1,'A,B are Monophyletic');
112 -outgroup => $d),1,'B,F are not Monophyletic' );
115 -outgroup => $f),1, 'A,B are Monophyletic');
120 -outgroup => $d), 1,'A,B,C are not Monophyletic w D as outgroup');
123 -outgroup => $i), 1, 'A,F,E are monophyletic with I as outgroup');
143 is($tree->reroot($a),1, 'Can re-root with A as outgroup');
/dports/biology/py-biopython/biopython-1.79/Bio/Nexus/
H A DTrees.py783 def root_with_outgroup(self, outgroup=None): argument
810 if outgroup is None:
812 outgroup_node = self.is_monophyletic(outgroup)
865 self, bstrees=None, constree=None, threshold=0.5, outgroup=None argument
880 if outgroup is None:
884 outgroup = self.get_taxa(smallest[1])
888 self.root_with_outgroup(outgroup)
891 constree = consensus(bstrees, threshold=threshold, outgroup=outgroup)
895 constree.root_with_outgroup(outgroup)
903 def consensus(trees, threshold=0.5, outgroup=None): argument
[all …]
/dports/cad/qflow/qflow-1.4.98/scripts/
H A Dpinmanager.py.in863 outgroup = self.uncompress_group(group)
866 if len(outgroup['pins']) > 0:
867 … print('padgroup ' + outgroup['name'] + ' ' + outgroup['permute'], file=ofile)
868 for pin, fixed in zip(outgroup['pins'], outgroup['fixed']):
870 if outgroup['sides'] != '':
871 print('restrict side ' + outgroup['sides'], file=ofile)
872 if outgroup['start'] != 0 or outgroup['stop'] != 100:
873 fstart = str(outgroup['start'] / 100.0)
874 fstop = str(outgroup['stop'] / 100.0)
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Tree/
H A DTreeFunctionsI.pm898 my ($nodes,$outgroup) = $self->_rearrange([qw(NODES OUTGROUP)],@args);
900 if( ! defined $nodes || ! defined $outgroup ) {
915 my $og_ancestor = $outgroup->ancestor;
945 my ($nodes,$outgroup) = $self->_rearrange([qw(NODES OUTGROUP)],@args);
947 if( ! defined $nodes || ! defined $outgroup ) {
971 my $og_ancestor = $outgroup->ancestor;
/dports/science/luscus/luscus_0.8.6/
H A Dfindsym.c80 char *outgroup, INT outsym[], INT *ierr ) { in findsym() argument
367 find_point_group(IN_GATE,ou,&x,what0,outgroup,outsym,0); in findsym()
372 if(find_point_group(IN_GATE,ou,&x,what,outgroup,outsym,1)) in findsym()
390 find_point_group_unscrambled(IN_GATE,ou,&x,what0,outgroup,outsym,0); in findsym()
398 rank_m=mycount(outgroup,' '); in findsym()
400 rank_f=mycount(outgroup,' '); in findsym()
405 find_point_group(IN_GATE,ou,&x,what,outgroup,outsym,0); in findsym()
1144 strcpy(outgroup,"x y z"); in find_point_group_2()
1162 outgroup[0]=0; in find_point_group_2()
1169 strcat(outgroup,oplab[p[k].gen[i]]); in find_point_group_2()
[all …]
/dports/biology/graphlan/nsegata-graphlan-66ec7cfce81e/pyphlan/
H A Dpyphlan.py36 outgroup = new_root
37 outgroup_path = tree.get_path(outgroup)
41 prev_blen = outgroup.branch_length
42 if outgroup.is_terminal():
44 outgroup.branch_length = 0.0
46 branch_length=tree.root.branch_length, clades=[outgroup])
53 parent.clades.pop(parent.clades.index(outgroup))
59 new_root = outgroup
74 if outgroup in old_root.clades:
76 old_root.clades.pop(old_root.clades.index(outgroup))
/dports/biology/graphlan/nsegata-pyphlan-eae40ebc0030/
H A Dpyphlan.py36 outgroup = new_root
37 outgroup_path = tree.get_path(outgroup)
41 prev_blen = outgroup.branch_length
42 if outgroup.is_terminal():
44 outgroup.branch_length = 0.0
46 branch_length=tree.root.branch_length, clades=[outgroup])
53 parent.clades.pop(parent.clades.index(outgroup))
59 new_root = outgroup
74 if outgroup in old_root.clades:
76 old_root.clades.pop(old_root.clades.index(outgroup))
/dports/biology/graphlan/nsegata-graphlan-66ec7cfce81e/src/
H A Dpyphlan.py36 outgroup = new_root
37 outgroup_path = tree.get_path(outgroup)
41 prev_blen = outgroup.branch_length
42 if outgroup.is_terminal():
44 outgroup.branch_length = 0.0
46 branch_length=tree.root.branch_length, clades=[outgroup])
53 parent.clades.pop(parent.clades.index(outgroup))
59 new_root = outgroup
74 if outgroup in old_root.clades:
76 old_root.clades.pop(old_root.clades.index(outgroup))
/dports/www/rt50/rt-5.0.2/t/api/
H A Dsavedsearch.t45 my $outgroup = RT::Group->new(RT->SystemUser);
46 $outgroup->CreateUserDefinedGroup(Name => 'searchgroup2'.$$);
47 $outgroup->AddMember(RT->SystemUser->Id);
100 ($ret, $msg) = $othersearch->Save(Privacy => 'RT::Group-' . $outgroup->Id,
110 ($ret, $msg) = $othersearch->Save(Privacy => 'RT::Group-' . $outgroup->Id,

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