ajphylo.c

Function ajPhyloDistNew

Constructor for AjPPhyloDist

Synopsis

Prototype
AjPPhyloDist ajPhyloDistNew (
      void
);

TypeNameRead/WriteDescription
AjPPhyloDist RETURNAjPPhyloDist object

Returns
AjPPhyloDist:AjPPhyloDist object

Description

Constructor for AjPPhyloDist

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloFreqNew

Constructor for AjPPhyloFreq

Synopsis

Prototype
AjPPhyloFreq ajPhyloFreqNew (
      void
);

TypeNameRead/WriteDescription
AjPPhyloFreq RETURNAjPPhyloFreq object

Returns
AjPPhyloFreq:AjPPhyloFreq object

Description

Constructor for AjPPhyloFreq

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloPropNew

Constructor for AjPPhyloProp

Synopsis

Prototype
AjPPhyloProp ajPhyloPropNew (
      void
);

TypeNameRead/WriteDescription
AjPPhyloProp RETURNAjPPhyloProp object

Returns
AjPPhyloProp:AjPPhyloProp object

Description

Constructor for AjPPhyloProp

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloStateNew

Constructor for AjPPhyloState

Synopsis

Prototype
AjPPhyloState ajPhyloStateNew (
      void
);

TypeNameRead/WriteDescription
AjPPhyloState RETURNAjPPhyloState object

Returns
AjPPhyloState:AjPPhyloState object

Description

Constructor for AjPPhyloState

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloTreeNew

Constructor for AjPPhyloTree

Synopsis

Prototype
AjPPhyloTree ajPhyloTreeNew (
      void
);

TypeNameRead/WriteDescription
AjPPhyloTree RETURNAjPPhyloTree object

Returns
AjPPhyloTree:AjPPhyloTree object

Description

Constructor for AjPPhyloTree

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloDistDel

Destructor for AjPPhyloDist

Synopsis

Prototype
void ajPhyloDistDel (
      AjPPhyloDist* pthis
);

TypeNameRead/WriteDescription
AjPPhyloDist*pthisDeleteDistance object
void RETURN

Output
pthis:(Delete)Distance object
Returns
void:No return value

Description

Destructor for AjPPhyloDist

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloFreqDel

Destructor for AjPPhyloFreq

Synopsis

Prototype
void ajPhyloFreqDel (
      AjPPhyloFreq* pthis
);

TypeNameRead/WriteDescription
AjPPhyloFreq*pthisDeletefrequency object
void RETURN

Output
pthis:(Delete)frequency object
Returns
void:No return value

Description

Destructor for AjPPhyloFreq

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloPropDel

Destructor for AjPPhyloProp

Synopsis

Prototype
void ajPhyloPropDel (
      AjPPhyloProp* pthis
);

TypeNameRead/WriteDescription
AjPPhyloProp*pthisDeleteProperties object
void RETURN

Output
pthis:(Delete)Properties object
Returns
void:No return value

Description

Destructor for AjPPhyloProp

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloStateDel

Destructor for AjPPhyloState

Synopsis

Prototype
void ajPhyloStateDel (
      AjPPhyloState* pthis
);

TypeNameRead/WriteDescription
AjPPhyloState*pthisDeleteDiscrete states object
void RETURN

Output
pthis:(Delete)Discrete states object
Returns
void:No return value

Description

Destructor for AjPPhyloState

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloStateDelarray

Destructor for AjPPhyloState array

Synopsis

Prototype
void ajPhyloStateDelarray (
      AjPPhyloState** pthis
);

TypeNameRead/WriteDescription
AjPPhyloState**pthisDeleteStates object array
void RETURN

Output
pthis:(Delete)States object array
Returns
void:No return value

Description

Destructor for AjPPhyloState array

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloTreeDel

Destructor for AjPPhyloTree

Synopsis

Prototype
void ajPhyloTreeDel (
      AjPPhyloTree* pthis
);

TypeNameRead/WriteDescription
AjPPhyloTree*pthisDeleteTrees object
void RETURN

Output
pthis:(Delete)Trees object
Returns
void:No return value

Description

Destructor for AjPPhyloTree

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloTreeDelarray

Destructor for AjPPhyloTree array

Synopsis

Prototype
void ajPhyloTreeDelarray (
      AjPPhyloTree** pthis
);

TypeNameRead/WriteDescription
AjPPhyloTree**pthisDeleteTrees object array
void RETURN

Output
pthis:(Delete)Trees object array
Returns
void:No return value

Description

Destructor for AjPPhyloTree array

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloDistRead

Reads phylogenetic distance matrix from a file

Synopsis

Prototype
AjPPhyloDist* ajPhyloDistRead (
      const AjPStr filename,
      ajint size,
      AjBool missing
);

TypeNameRead/WriteDescription
const AjPStrfilenameInputinput filename
ajintsizeInputNumber of rows in distance matrix
AjBoolmissingInputMissing values (replicates zero) allowed
AjPPhyloDist* RETURNPhylogenetic distances object on success NULL on failure

Input
filename:(Input)input filename
size:(Input)Number of rows in distance matrix
missing:(Input)Missing values (replicates zero) allowed
Returns
AjPPhyloDist*:Phylogenetic distances object on success NULL on failure

Description

Reads phylogenetic distance matrix from a file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloDistTrace

Reports phylogenetic distance data to the debug file

Synopsis

Prototype
void ajPhyloDistTrace (
      const AjPPhyloDist thys
);

TypeNameRead/WriteDescription
const AjPPhyloDistthysInputPhylogenetic frequencies object
void RETURN

Input
thys:(Input)Phylogenetic frequencies object
Returns
void:No return value

Description

Reports phylogenetic distance data to the debug file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloFreqRead

Reads phylogenetic frequencies from a file

Synopsis

Prototype
AjPPhyloFreq ajPhyloFreqRead (
      const AjPStr filename,
      AjBool contchar,
      AjBool genedata,
      AjBool indiv
);

TypeNameRead/WriteDescription
const AjPStrfilenameInputinput filename
AjBoolcontcharInputContinuous character data expected
AjBoolgenedataInputGene frequency data expected
AjBoolindivInputMultiple individuals for one name only for continuous character data.
AjPPhyloFreq RETURNPhylogenetic frequencies object on success NULL on failure

Input
filename:(Input)input filename
contchar:(Input)Continuous character data expected
genedata:(Input)Gene frequency data expected
indiv:(Input)Multiple individuals for one name only for continuous character data.
Returns
AjPPhyloFreq:Phylogenetic frequencies object on success NULL on failure

Description

Reads phylogenetic frequencies from a file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloFreqTrace

Reports phylogenetic frequencies data to the debug file

Synopsis

Prototype
void ajPhyloFreqTrace (
      const AjPPhyloFreq thys
);

TypeNameRead/WriteDescription
const AjPPhyloFreqthysInputPhylogenetic frequencies object
void RETURN

Input
thys:(Input)Phylogenetic frequencies object
Returns
void:No return value

Description

Reports phylogenetic frequencies data to the debug file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloPropRead

Reads phylogenetic properties (weights, factors, ancestral states) from a file

Synopsis

Prototype
AjPPhyloProp ajPhyloPropRead (
      const AjPStr filename,
      const AjPStr propchars,
      ajint len,
      ajint size
);

TypeNameRead/WriteDescription
const AjPStrfilenameInputinput filename
const AjPStrpropcharsInputValid property characters
ajintlenInputLength of properties string
ajintsizeInputNumber of property sets expected If zero, read first only or whatever the file says
AjPPhyloProp RETURNPhylogenetic properties object on success NULL on failure

Input
filename:(Input)input filename
propchars:(Input)Valid property characters
len:(Input)Length of properties string
size:(Input)Number of property sets expected If zero, read first only or whatever the file says
Returns
AjPPhyloProp:Phylogenetic properties object on success NULL on failure

Description

Reads phylogenetic properties (weights, factors, ancestral states) from a file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloPropGetSize

Returns size (number of property strings)

Synopsis

Prototype
ajint ajPhyloPropGetSize (
      const AjPPhyloProp thys
);

TypeNameRead/WriteDescription
const AjPPhyloPropthysInputProperties object
ajint RETURNNumber of property strings

Input
thys:(Input)Properties object
Returns
ajint:Number of property strings

Description

Returns size (number of property strings)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloPropTrace

Reports phylogenetic property data to the debug file

Synopsis

Prototype
void ajPhyloPropTrace (
      const AjPPhyloProp thys
);

TypeNameRead/WriteDescription
const AjPPhyloPropthysInputPhylogenetic frequencies object
void RETURN

Input
thys:(Input)Phylogenetic frequencies object
Returns
void:No return value

Description

Reports phylogenetic property data to the debug file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloStateRead

Reads phylogenetic discrete states from a file

Synopsis

Prototype
AjPPhyloState* ajPhyloStateRead (
      const AjPStr filename,
      const AjPStr statechars
);

TypeNameRead/WriteDescription
const AjPStrfilenameInputinput filename
const AjPStrstatecharsInputValid state characters
AjPPhyloState* RETURNPhylogenetic discrete states object on success NULL on failure

Input
filename:(Input)input filename
statechars:(Input)Valid state characters
Returns
AjPPhyloState*:Phylogenetic discrete states object on success NULL on failure

Description

Reads phylogenetic discrete states from a file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloStateTrace

Reports phylogenetic discrete state data to the debug file

Synopsis

Prototype
void ajPhyloStateTrace (
      const AjPPhyloState thys
);

TypeNameRead/WriteDescription
const AjPPhyloStatethysInputPhylogenetic discrete states object
void RETURN

Input
thys:(Input)Phylogenetic discrete states object
Returns
void:No return value

Description

Reports phylogenetic discrete state data to the debug file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloTreeRead

Reads phylogenetic trees from a file.

For background see the NESCent Hackathon Wiki https://www.nescent.org/wg_phyloinformatics/Main_Page

Programs using or producing trees include:

Editors in http://bioinfo.unice.fr/biodiv/Tree_editors.html

Packages PHYLIP, GARLI, MrBayes, PROTML, TREE-PUZZLE PAUP

Tree formats include:

Newick (New Hampshire) is a simple string with parentheses see http://evolution.genetics.washington.edu/phylip/newicktree.html and http://evolution.genetics.washington.edu/phylip/newick_doc.html Newick format is used by PHYLIP, GARLI, MrBayes, PROTML, TREE-PUZZLE In PAUP the format is called "phylip" Phylip includes weights for multiple input trees as a final comment containing only a floating point number e.g. [0.5];

Nexus files use Translate to define numbers, and then have a Newick string using the numbers, or simply define the Newick string with names. The branch lengths appear as in Newick. http://workshop.molecularevolution.org/resources/fileformats/tree_formats.php Test files (including malformed ones) are available from https://www.nescent.org/wg_phyloinformatics/Supporting_NEXUS

nhx (New Hampshire Extended) includes annotation using specially formatted comments after the name:length in the form [&&NHX:code=value;code=value] where codes are documented in http://www.phylosoft.org/forester/NHX.html according to some documentation, ATV and FORESTER can read NHX with the [] removed but this is deprecated (naturally, as this would be a valid Newick tree with proper comments). NHX also bans the use of empty nodes so names are required. Apparently PHYLIP can read trees with no names.

svggraph is an output format only (or at least, no sign of anything reading it)

tabtree is an ASCII text representation used for output only by BioPerl::TreeIO

lintree is a program output format. The program is available from http://www.bio.psu.edu/People/Faculty/Nei/Lab/lintre/lintre.unix.tar.Z

phyloXML is an effort to define an XML format, still in progress http://www.phyloxml.org/

TGF treegraph format http://www.math.uni-bonn.de/people/jmueller/extra/treegraph/docu.pdf

TGF TreeDyn format ... not the same as treegraph http://www.treedyn.org/

Synopsis

Prototype
AjPPhyloTree* ajPhyloTreeRead (
      const AjPStr filename,
      ajint size
);

TypeNameRead/WriteDescription
const AjPStrfilenameInputinput filename
ajintsizeInputNumber of trees expected If zero, read all trees
AjPPhyloTree* RETURNPhylogenetic tree object array on success NULL on failure

Input
filename:(Input)input filename
size:(Input)Number of trees expected If zero, read all trees
Returns
AjPPhyloTree*:Phylogenetic tree object array on success NULL on failure

Description

Reads phylogenetic trees from a file.

For background see the NESCent Hackathon Wiki https://www.nescent.org/wg_phyloinformatics/Main_Page

Programs using or producing trees include:

Editors in http://bioinfo.unice.fr/biodiv/Tree_editors.html

Packages PHYLIP, GARLI, MrBayes, PROTML, TREE-PUZZLE PAUP

Tree formats include:

Newick (New Hampshire) is a simple string with parentheses see http://evolution.genetics.washington.edu/phylip/newicktree.html and http://evolution.genetics.washington.edu/phylip/newick_doc.html Newick format is used by PHYLIP, GARLI, MrBayes, PROTML, TREE-PUZZLE In PAUP the format is called "phylip" Phylip includes weights for multiple input trees as a final comment containing only a floating point number e.g. [0.5];

Nexus files use Translate to define numbers, and then have a Newick string using the numbers, or simply define the Newick string with names. The branch lengths appear as in Newick. http://workshop.molecularevolution.org/resources/fileformats/tree_formats.php Test files (including malformed ones) are available from https://www.nescent.org/wg_phyloinformatics/Supporting_NEXUS

nhx (New Hampshire Extended) includes annotation using specially formatted comments after the name:length in the form [&&NHX:code=value;code=value] where codes are documented in http://www.phylosoft.org/forester/NHX.html according to some documentation, ATV and FORESTER can read NHX with the [] removed but this is deprecated (naturally, as this would be a valid Newick tree with proper comments). NHX also bans the use of empty nodes so names are required. Apparently PHYLIP can read trees with no names.

svggraph is an output format only (or at least, no sign of anything reading it)

tabtree is an ASCII text representation used for output only by BioPerl::TreeIO

lintree is a program output format. The program is available from http://www.bio.psu.edu/People/Faculty/Nei/Lab/lintre/lintre.unix.tar.Z

phyloXML is an effort to define an XML format, still in progress http://www.phyloxml.org/

TGF treegraph format http://www.math.uni-bonn.de/people/jmueller/extra/treegraph/docu.pdf

TGF TreeDyn format ... not the same as treegraph http://www.treedyn.org/

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloTreeTrace

Reports phylogenetic discrete state data to the debug file

Synopsis

Prototype
void ajPhyloTreeTrace (
      const AjPPhyloTree thys
);

TypeNameRead/WriteDescription
const AjPPhyloTreethysInputPhylogenetic discrete states object
void RETURN

Input
thys:(Input)Phylogenetic discrete states object
Returns
void:No return value

Description

Reports phylogenetic discrete state data to the debug file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajPhyloExit

Cleans up phylogenetic data internal memory

Synopsis

Prototype
void ajPhyloExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleans up phylogenetic data internal memory

See Also

See other functions in this section

Availability

In release 6.4.0