| Bio::TreeIO::lintree(3pm) | User Contributed Perl Documentation | Bio::TreeIO::lintree(3pm) |
Bio::TreeIO::lintree - Parser for lintree output trees
# do not use directly, use through Bio::TreeIO
use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(-format => 'lintree',
-file => 't/data/crab.nj');
my $tree = $treeio->next_tree;
Parser for the lintree output which looks like this
13 sequences 1000 bootstraping 1 A-salina 2 C-vittat 3 C-sp. 4 L-aequit 5 P-camtsc 6 E-tenuim 7 L-splend 8 P-bernha 9 P-acadia 10 P-p(NE) 11 P-p(GU) 12 P-l(NE) 13 P-l(GU) 14 and 2 0.098857 1000 14 and 3 0.127932 1000 15 and 1 0.197471 1000 15 and 14 0.029273 874 16 and 10 0.011732 1000 16 and 11 0.004529 1000 17 and 12 0.002258 1000 17 and 13 0.000428 1000 18 and 16 0.017512 1000 18 and 17 0.010824 998 19 and 4 0.006534 1000 19 and 5 0.006992 1000 20 and 15 0.070461 1000 20 and 18 0.030579 998 21 and 8 0.003339 1000 21 and 9 0.002042 1000 22 and 6 0.011142 1000 22 and 21 0.010693 983 23 and 20 0.020714 996 23 and 19 0.020350 1000 24 and 23 0.008665 826 24 and 22 0.013457 972 24 and 7 0.025598 1000
See http://www.bio.psu.edu/People/Faculty/Nei/Lab/software.htm for access to the program and N Takezaki, A Rzhetsky, and M Nei, "Phylogenetic test of the molecular clock and linearized trees." Mol Biol Evol 12(5):823-33.
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Ideas and discussion from:
Alan Christoffels
Avril Coghlan
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::TreeIO::lintree->new(); Function: Builds a new Bio::TreeIO::lintree object Returns : an instance of Bio::TreeIO::lintree Args : -nodetype => Node type to create [default Bio::Tree::Node]
Title : next_tree Usage : my $tree = $treeio->next_tree Function: Gets the next tree in the stream Returns : Bio::Tree::TreeI Args : none
Title : nodetype Usage : $obj->nodetype($newval) Function: Example : Returns : value of nodetype (a scalar) Args : on set, new value (a scalar or undef, optional)
| 2021-08-15 | perl v5.32.1 |