pal.alignment.*
-
public static final char
'-'
"---"
"_-?."
public static final char
'?'
"???"
-
public static final double
0d/0d
pal.coalescent.*
-
public static final int
0
public static final int
1
public static final int
2
-
public static final int
0
public static final int
2
public static final int
1
pal.datatype.*
-
public static final char
'*'
public static final int
21
-
public static final int
13
public static final int
9
public static final int
12
public static final int
11
public static final int
6
public static final int
7
public static final int
8
public static final int
10
public static final int
5
public static final int
3
public static final int
4
public static final int
0
public static final int
1
public static final int
2
-
"amino acid"
public static final int
1
"codon"
public static final int
4
public static final int
5
"gap balanced"
"nucleotide"
public static final int
3
"nucleotide"
public static final int
0
public static final int
6
public static final char
'-'
public static final int
-2
public static final int
-1
"binary"
public static final int
2
public static final int
100
public static final char
'?'
"???"
-
public static final int
0
public static final int
1
public static final int
2
public static final int
3
pal.eval.*
-
public static final int
3
pal.gui.*
-
public static final int
1
public static final int
0
public static final int
2
-
public static final int
1
public static final int
3
public static final int
0
public static final int
2
-
"bootstrap"
"times"
public static final int
15
public static final int
0
-
public static final int
30
public static final int
10
public static final int
75
public static final int
20
public static final int
10
public static final int
20
-
public static final int
30
public static final int
15
public static final int
10
public static final int
10
public static final int
20
public static final int
4
public static final int
20
pal.io.*
-
public static final char
'+'
public static final char
'*'
public static final char
'\\'
public static final char
'`'
public static final char
'\r'
public static final char
':'
public static final char
','
public static final char
'\"'
public static final char
'-'
public static final char
'='
public static final char
'/'
public static final char
'>'
public static final char
'#'
15
public static final char
'{'
public static final char
'['
public static final char
'\n'
public static final char
'('
public static final char
'<'
public static final int
13
public static final char
'.'
public static final int
12
public static final char
'}'
public static final char
']'
public static final char
')'
public static final char
'\''
public static final char
';'
public static final char
' '
public static final char
'\t'
public static final int
10
public static final int
14
public static final int
1
public static final int
11
public static final int
2
public static final int
0
pal.math.*
-
public static final int
2
public static final int
0
public static final int
1
pal.mep.*
-
"Incompatible intervals"
"Max time is "
"Negative values"
"Repeated times"
"Zero time"
pal.misc.*
-
"boolean"
"double"
"float"
"integer"
"string"
-
public static final double
5.0E-7
public static final double
0.04
public static final int
6
public static final double
1.0
public static final double
1.0E-9
-
"November, 2004"
"PAL 1.51"
-
public static final int
2
public static final int
0
public static final int
1
public static final int
3
public static final int
5
public static final int
6
public static final int
4
pal.substmodel.*
-
public static final int
3
public static final int
6
public static final int
0
public static final int
1
public static final int
7
public static final int
2
public static final int
4
public static final int
5
-
public static final int
0
-
public static final int
0
-
public static final int
4
public static final int
3
public static final int
0
public static final int
2
public static final int
5
public static final int
1
-
public static final int
0
public static final int
1
-
public static final double
2.0
public static final double
1.0
public static final int
0
public static final double
100.0
public static final double
100.0
public static final double
1.0E-6
public static final double
0.0
public static final int
1
-
public static final double
0.5
public static final double
0.0
public static final double
1.0
pal.tree.*
-
"clade probability"
"mean clade height"
"node height SE"
"subtree probability"
-
public static final int
200
public static final int
100
public static final int
300
pal.treesearch.*
-
public static final int
4
public static final int
0
public static final double
0.01
public static final int
2
public static final int
3
public static final int
1
public static final int
6
public static final double
10.0
public static final double
0.0
public static final int
5
-
public static final int
3
public static final int
0
public static final int
1
public static final int
2
pal.util.*
-
"A-C"
"A-G"
"A-T"
"alignment"
"alpha"
"ancestral mutation rate"
"ancestral population size"
"att"
"backwards"
"BLOSUM62"
"C-G"
"C-T"
"coalescent"
"constexpconst"
"constexp"
"constant"
"constant"
"CPREV"
"tx"
"datatype"
"datatypeid"
"Dayhoff"
"days"
"demographicmodel"
"direction"
"edge"
"expanding"
"exponential"
"F81"
"F84"
"frequencies"
"G-T"
"shape"
"gamma"
"generations"
"lx"
"growth rate"
"GTR"
"height"
"HKY"
"id"
"JC"
"JTT"
"kappa"
"length"
"missing"
"model"
"months"
"MTREV24"
"step time"
"current mutation rate"
"mutationratemodel"
"mutations"
"name"
"node"
"ncat"
"omega"
"origin"
"parameter"
"current population size"
"prymidine/purine transition ratio"
"ratedistribution"
"ratematrix"
"sequence"
public static final int
4
"stepped"
"time"
"timedata"
"Tamura-Nei"
"tree"
"transition/transversion ratio"
"binary"
"type"
"uniform"
"uniform"
"units"
"unknown"
"value"
"VT"
"WAG"
"Yang codon model"
"years"