ajphylo

Data type AjPPhyloDist

Input can be square (all values) or lower-triangular (diagonal and below) or upper-triangular (diagonal and above). We can count values for the first 2 species to identify the format.

S-format allows degree of replication for each distance (integer) we can check for this (twice as many numbers) otherwise we set the replicates to 1.

Alias name(s)

Name
AjSPhyloDist
AjOPhyloDist

Attributes

Name	Type	Description
Size	ajint	Size - number of rows and number of columns
HasReplicates	AjBool	Has (some) replicates data in file
Names	AjPStr*	Row names, NULL at end
Data	float*	Distance matrix Size*Size with diagonal 0.0
Replicates	ajint*	Replicate count default=1 missing=0
HasMissing	AjBool	Has missing data in file
Padding	char[4]	Padding to alignment boundary

Data type AjPPhyloFreq

For continuous data there are always 2 alleles For gene frequency data there can be more than 2 alleles

Alias name(s)

Name
AjSPhyloFreq
AjOPhyloFreq

Attributes

Name	Type	Description
Size	ajint	Number of rows
Loci	ajint	Number of loci per name
Len	ajint	Number of values per name may be more than 1 per locus
ContChar	AjBool	Continuous character data if true
Names	AjPStr*	Row names array (size is Size)

Attributes

Name	Type	Description
Species	ajint*	Species number 1, 2, 3 for each value array size is Len
Individuals	ajint*	Allele countNumber of individuals 1 or more per species array size is Loci

Attributes

Name	Type	Description
Locus	ajint*	Locus number 1, 2, 3 for each value array size is Len
Allele	ajint*	Allele count 2 or more per locus array size is Loci
Data	float*	Frequency for each allele for each Name
Within	AjBool	Individual data within species if true
Padding	char[4]	Padding to alignment boundary

Data type AjPPhyloProp

Basically, all of these are one value per position

Weights are converted to integers 0-9, A=10 Z=35 by phylip There are programs that can use multiple weights We can handle this by making all of these multiple, and using ACD to limit them to 1 for non-weight data.

Ancestral states are character data

Factors are multi-state character data where the factor character changes when moving to a new character. Without this, all factors are assumed to be different. The default would be to make each character distinct by alternating 12121212 or to use 12345678901234567890.

We can, in fact, convert any input string into this format for factors but probably we can leave them unchanged.

Alias name(s)

Name
AjSPhyloProp
AjOPhyloProp

Attributes

Name	Type	Description
Len	ajint	string length
Size	ajint	number of strings
IsWeight	AjBool	is phylip weight values if true
IsFactor	AjBool	is phylip factor values if true
Str	AjPStr*	The original string(s)

Data type AjPPhyloState

Basically, all of these are one value per position

States have a limited character set, usually defined through ACD

Alias name(s)

Name
AjSPhyloState
AjOPhyloState

Attributes

Name	Type	Description
Len	ajint	string length
Size	ajint	number of strings
Characters	AjPStr	The allowed state characters
Names	AjPStr*	The names
Str	AjPStr*	The original string(s)
Count	ajint	number of enzymes for restriction data
Padding	char[4]	Padding to alignment boundary

Data type AjPPhyloTree

For programs that read multiple tree inputs we use an array, and let ACD limit the others to 1 tree.

Alias name(s)

Name
AjSPhyloTree
AjOPhyloTree

Attributes

Name	Type	Description
Multifurcated	AjBool	Multifurcating (..(a,b,c)..)
BaseTrifurcated	AjBool	3-way base (a,b,c)
BaseBifurcated	AjBool	Rooted 2-way base (a,b)
BaseQuartet	AjBool	Unrooted quartet ((a,b),(c,d));
HasLengths	AjBool	Tree has branch lengths
Size	ajint	Number of nodes
Tree	AjPStr	Newick tree string