.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "Bio::TreeIO::lintree 3pm" .TH Bio::TreeIO::lintree 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::TreeIO::lintree \- Parser for lintree output trees .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 5 \& # do not use directly, use through Bio::TreeIO \& use Bio::TreeIO; \& my $treeio = Bio::TreeIO\->new(\-format => \*(Aqlintree\*(Aq, \& \-file => \*(Aqt/data/crab.nj\*(Aq); \& my $tree = $treeio\->next_tree; .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" Parser for the lintree output which looks like this .PP .Vb 10 \& 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 .Ve .PP 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, \*(L"Phylogenetic test of the molecular clock and linearized trees.\*(R" Mol Biol Evol 12(5):823\-33. .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "Mailing Lists" User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: .PP \&\fIbioperl\-l@bioperl.org\fR .PP rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. .SS "Reporting Bugs" .IX Subsection "Reporting Bugs" Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR \- Jason Stajich" .IX Header "AUTHOR - Jason Stajich" Email jason-at-bioperl-dot-org .SH "CONTRIBUTORS" .IX Header "CONTRIBUTORS" Ideas and discussion from: Alan Christoffels Avril Coghlan .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SS "new" .IX Subsection "new" .Vb 5 \& 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] .Ve .SS "next_tree" .IX Subsection "next_tree" .Vb 5 \& Title : next_tree \& Usage : my $tree = $treeio\->next_tree \& Function: Gets the next tree in the stream \& Returns : Bio::Tree::TreeI \& Args : none .Ve .SS "nodetype" .IX Subsection "nodetype" .Vb 6 \& Title : nodetype \& Usage : $obj\->nodetype($newval) \& Function: \& Example : \& Returns : value of nodetype (a scalar) \& Args : on set, new value (a scalar or undef, optional) .Ve